Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.
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机译：跨膜蛋白在信号传导，离子转运，营养吸收以及维持细胞内部和外部环境之间的动态平衡方面起着至关重要的作用。尽管它们具有重要的生物学功能和丰度，但所有确定的结构中只有不到2％是跨膜蛋白。鉴于与跨膜蛋白的高分辨率结构确定相关的持续技术难题，包括计算和实验技术在内的其他方法对于增进我们对它们的拓扑结构，3D结构，功能和相互作用的理解仍然至关重要。在这里，我们报告了一种基于LC / MS / MS的表面标记和生物素捕获的肽片段鉴定的高通量测定跨膜蛋白胞外区段的方法。我们表明，可靠的细胞外蛋白片段鉴定可以提高现有拓扑预测算法的准确性和可靠性。使用实验拓扑数据作为约束条件，我们改进的预测工具为数百种人类跨膜蛋白提供了准确而可靠的拓扑模型。
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