Stepwise design of pseudosymmetric protein hetero-oligomers.
Stepwise design of pseudosymmetric protein hetero-oligomers.
复制标题
假对称蛋白质异源寡聚物的逐步设计。
DOI：
10.1101/2023.04.07.535760
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Baker,David
中科院分区：
文献类型：
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作者：
Kibler,RyanD;Lee,Sangmin;Kennedy,MadisonA;Wicky,BasileIM;Lai,StellaM;Kostelic,MariusM;Li,Xinting;Chow,CameronM;Carter,Lauren;Wysocki,VickiH;Stoddard,BarryL;Baker,David
具有三个或更多具有整体结构（而非序列）对称性的独特亚基的假对称异源寡聚物在生物学中发挥着关键作用，从头生成此类蛋白质的系统方法将为控制细胞信号传导和设计复杂蛋白质材料提供新途径。然而，具有三个或更多结构几乎相同的不同链的蛋白质异质寡聚物的从头设计是一个具有挑战性的问题，因为它需要同时准确设计多个蛋白质-蛋白质界面。在这里，我们描述了一种分而治之的方法，将多界面设计挑战分解为一组更容易处理的对称单界面重新设计问题，然后将经过验证的同源低聚物结构重组为假对称异源低聚物。从头设计由9或24个串联重复单元组成的环状同源低聚物开始，我们重新设计了亚基间界面，生成了15种新的同源低聚物，并将它们重组形成17种新的异源低聚物，包括ABC异源三聚体、A2B2异源四聚体以及具有高结构特异性组装的A3B3和A2B2C2异源六聚体。每个系统生成的对称同质低聚物和假对称异质低聚物共享一个共同的主链，因此是生成和功能化更大对称组件的理想构建块。
Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials. However, the de novo design of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign problems, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting from de novo designed circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 15 new homo-oligomers and recombined them to make 17 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system share a common backbone, and hence are ideal building blocks for generating and functionalizing larger symmetric assemblies.