伪对称蛋白质异源寡聚体的设计

Design of pseudosymmetric protein hetero-oligomers.

作者信息

Kibler Ryan D, Lee Sangmin, Kennedy Madison A, Wicky Basile I M, Lai Stella M, Kostelic Marius M, Carr Ann, Li Xinting, Chow Cameron M, Nguyen Tina K, Carter Lauren, Wysocki Vicki H, Stoddard Barry L, Baker David

机构信息

Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.

Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.

出版信息

Nat Commun. 2024 Dec 18;15(1):10684. doi: 10.1038/s41467-024-54913-8.

Abstract

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 unsolved 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 tasks, 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 19 new homo-oligomers and structurally recombined them to make 24 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 have identical or nearly identical backbones, and hence are ideal building blocks for generating and functionalizing larger symmetric and pseudosymmetric assemblies.

摘要

具有三个或更多独特亚基且具有整体结构(而非序列)对称性的假对称杂聚体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,从头设计具有三个或更多具有几乎相同结构的不同链的蛋白质杂聚体是一个具有挑战性的未解决问题,因为它需要同时精确设计多个蛋白质-蛋白质界面。在这里,我们描述了一种分而治之的方法,该方法将多界面设计挑战分解为一组更易于处理的对称单界面重新设计任务,然后将经过验证的同聚体进行结构重组,形成假对称杂聚体。从由9个或24个串联重复单元组成的从头设计的环状同聚体开始,我们重新设计了亚基间界面,生成了19种新的同聚体,并对其进行结构重组,以制造24种新的杂聚体,包括ABC异源三聚体、A2B2异源四聚体以及A3B3和A2B2C2异源六聚体,它们以高度的结构特异性组装。为每个系统生成的对称同聚体和假对称杂聚体具有相同或几乎相同的主链,因此是生成更大的对称和假对称组装体并使其功能化的理想构建块。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/237e/11655659/45bc2b255c20/41467_2024_54913_Fig1_HTML.jpg

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