Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Nat Chem Biol. 2024 Aug;20(8):974-980. doi: 10.1038/s41589-024-01632-2. Epub 2024 May 30.
In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9-14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.
在天然蛋白质中，结构环在分子识别、信号转导和酶催化中起着核心作用。然而，由于环区的固有灵活性和不规则性，通过从头设计蛋白质来组织蛋白质功能部位的多个结构环一直非常困难。在这里，我们描述了一种解决方案，该方案设计了串联重复蛋白，这些蛋白具有由广泛氢键相互作用支撑的结构环（9-14 个残基）。实验特性表明，这些设计物是单分散的、高溶解性的、折叠的和热稳定的。晶体结构与设计模型非常吻合，环结构与设计相符。我们通过设计和表征用于扩展肽的结合物来证明环支撑提供的功能，其中环形成扩展结合口袋的一侧。设计多个结构环的能力应该有助于设计新的蛋白质功能。
