The ability to construct novel enzymes is a major aim in de novo protein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recently published de novo design of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a short de novo helix on top of the barrel. Due to the size of the protein we developed a design pipeline based on computational ab initio folding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites.

中文翻译：

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通过合理设计的二级结构元件扩展从头TIM枪管

构建新酶的能力是从头蛋白质设计的主要目标。TIM筒是设计尝试中常用的酶折叠。这种折叠是酶的常见拓扑结构，可以包含许多不同的反应。最近发布的四重对称TIM枪管从头设计为潜在的酶设计提供了一个广为人知的最小支架。在这里，我们通过在枪管顶部增加一个从头开始的螺旋结构，探索扩展这种支架并使其多样化的机会。由于蛋白质的大小，我们开发了基于计算从头开始折叠的设计流水线，该设计流水线解决了围绕螺旋及其附近区域的较简单的子问题，并使它适应整个蛋白质。我们提供一种变体的生化特性和高分辨率X射线结构，并将其与我们的设计模型进行比较。