Department of Biology, Shahed University, Tehran, Iran.
Department of Biology, Shahed University, Tehran-Qom Express Way, Tehran, Iran.
Comput Biol Chem. 2018 Feb;72:77-86. doi: 10.1016/j.compbiolchem.2018.01.003. Epub 2018 Jan 12.
Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen metabolic fitness as well as its adherence and invasion to human epithelial cells. This protein is also involved in interaction of the bacteria with host cells by binding to fibronectin. Moreover, Omp33-36 renders cytotoxicity to A. baumannii in addition to inducing apoptosis and modulation of autophagy. In the present study, an integrated strategy is launched to pierce into the 3D structure of Omp33-36 protein. The signal peptide within the sequence was determined, then, topology as well as secondary and tertiary structures of the protein were predicted. The mature protein assigned as a 14-stranded barrel in which residues 1-19 is removed as signal peptide. The obtained 3D models were evaluated in terms of quality; and then, served as queries to find similar protein structures. The hits were analyzed regarding topology among which 14-stranded were considered. The most qualified model was refined and then its sequence aligned to its counterpart similar structure protein (CymA from Klebsiella oxytoca). The determined structure of Omp33-36 could justify its porin function and carbapenem-resistance associated with the loss of this protein.
鲍曼不动杆菌中的 Omp33-36 是一种与病原体代谢适应性以及其对人类上皮细胞的黏附和侵袭有关的毒力因子。这种蛋白质还通过与纤维连接蛋白结合参与细菌与宿主细胞的相互作用。此外，Omp33-36 除了诱导细胞凋亡和自噬的调节外，还对鲍曼不动杆菌具有细胞毒性。在本研究中，启动了一项综合策略来研究 Omp33-36 蛋白的三维结构。确定了序列中的信号肽，然后预测了该蛋白的拓扑结构以及二级和三级结构。成熟蛋白被指定为 14 股桶，其中 1-19 位残基被去除作为信号肽。获得的三维模型根据质量进行评估；然后，作为查询来寻找类似的蛋白质结构。根据拓扑结构对命中结果进行分析，其中考虑了 14 股。对最合格的模型进行了细化，然后将其序列与类似结构的蛋白质（来自产酸克雷伯氏菌的 CymA）进行比对。确定的 Omp33-36 结构可以证明其孔蛋白功能和与该蛋白丢失相关的碳青霉烯类药物耐药性。
