PDF(Pubmed)
Abstract：
We have been aware of the existence of knotted proteins for over 30 years-but it is hard to predict what is the most complicated knot that can be formed in proteins. Here, we show new and the most complex knotted topologies recorded to date-double trefoil knots (31 #31). We found five domain arrangements (architectures) that result in a doubly knotted structure in almost a thousand proteins. The double knot topology is found in knotted membrane proteins from the CaCA family, that function as ion transporters, in the group of carbonic anhydrases that catalyze the hydration of carbon dioxide, and in the proteins from the SPOUT superfamily that gathers 31 knotted methyltransferases with the active site-forming knot. For each family, we predict the presence of a double knot using AlphaFold and RoseTTaFold structure prediction. In the case of the TrmD-Tm1570 protein, which is a member of SPOUT superfamily, we show that it folds in vitro and is biologically active. Our results show that this protein forms a homodimeric structure and retains the ability to modify tRNA, which is the function of the single-domain TrmD protein. However, how the protein folds and is degraded remains unknown.
摘要：
我们已经意识到打结蛋白质的存在已经超过30年了，但是很难预测蛋白质中可以形成的最复杂的结是什么。这里,我们展示了新的和最复杂的打结拓扑记录到日期-双三叶结（31＃31）。我们发现了五个域排列（体系结构），它们导致近一千个蛋白质中的双重打结结构。在CaCA家族的打结膜蛋白中发现了双结拓扑结构，起到离子转运的作用，在催化二氧化碳水合的碳酸酐酶组中，以及来自SPOUT超家族的蛋白质中，该蛋白质收集了31个具有活性位点形成结的结的甲基转移酶。对于每个家庭，我们使用AlphaFold和RoseTTaFold结构预测来预测双结的存在。在TrmD-Tm1570蛋白的情况下，是SPOUT超家族的一员,我们表明它在体外折叠并且具有生物活性。我们的结果表明，这种蛋白质形成同源二聚体结构并保留修饰tRNA的能力，这是单结构域TrmD蛋白的功能。然而,蛋白质如何折叠和降解仍然未知。
