Paramasivam Nagarajan, Linke Dirk
Department 1, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany.
Computational Oncology, Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
Methods Mol Biol. 2015;1329:271-7. doi: 10.1007/978-1-4939-2871-2_21.
Well-structured proteins interact with other proteins through surface-surface interactions. In such cases, the residues that form the interacting surface are not necessarily neighboring residues on the level of protein sequence. In contrast, unfolded or partially unfolded proteins can interact with other proteins through defined linear motifs. In the case of the β-barrel assembly machinery (BAM) in the outer membrane of Gram-negative bacteria, unfolded β-barrel proteins are recognized through a C-terminal linear motif, and are inserted into the membrane. While the exact mechanism of recognition is still under investigation, it has been shown that mutations in the recognition motif can partially or completely abolish membrane insertion. In this chapter, we demonstrate the workflow for motif discovery, motif extraction, and motif visualization on the example of the C-terminal motifs in transmembrane β-barrel proteins.
结构良好的蛋白质通过表面与表面的相互作用与其他蛋白质相互作用。在这种情况下，形成相互作用表面的残基在蛋白质序列水平上不一定是相邻残基。相比之下，未折叠或部分未折叠的蛋白质可以通过确定的线性基序与其他蛋白质相互作用。在革兰氏阴性菌外膜中的β-桶组装机器（BAM）的情况下，未折叠的β-桶蛋白通过C端线性基序被识别，并插入膜中。虽然识别的确切机制仍在研究中，但已经表明识别基序中的突变可以部分或完全消除膜插入。在本章中，我们以跨膜β-桶蛋白的C端基序为例，展示基序发现、基序提取和基序可视化的工作流程。
