Lawrence Berkeley National Laboratory, Berkeley, California, United States.
J Proteome Res. 2012 Dec 7;11(12):5720-35. doi: 10.1021/pr300548d. Epub 2012 Oct 25.
Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.
细胞膜是细胞防御的“第一道防线”，也是细胞与其环境之间的界面。为了确定目标生物细胞膜中存在的蛋白质和蛋白质复合物的范围，我们利用一种“无标签”的方法来系统地分离和鉴定天然膜蛋白复合物。作为初步的研究对象，我们选择了革兰氏阴性硫酸盐还原菌脱硫弧菌。使用这种无标签的方法，我们已经鉴定出了预期的大约三分之二的外膜相关蛋白。其中大约四分之三似乎形成同源复合物。用于分析多个实验中汇总数据的统计和机器学习方法揭示了额外的蛋白质-蛋白质相互作用网络，这些网络提供了关于在细胞这一区域内蛋白质之间形成异源接触的深入了解。总的来说，这些结果建立了一个 D. vulgaris 外膜蛋白数据集，这对于检测和描述外膜蛋白质组中的环境驱动变化以及应激反应途径的建模至关重要。这里使用的工作流程应该可以有效地对各种生物体中的膜蛋白复合物进行全面描述。
