Center for Theoretical Biological Physics, University of California at San Diego, Gilman Drive 9500, La Jolla, CA 92037, USA.
Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17783-8. doi: 10.1073/pnas.1201804109. Epub 2012 Aug 13.
Recent experiments have conclusively shown that proteins are able to fold from an unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones. These experiments are consistent with a growing body of theoretical work showing that a funneled, minimally frustrated energy landscape is sufficient to fold small proteins with complex topologies. Here, we present a theoretical investigation of the folding of a knotted protein, 2ouf, engineered in the laboratory by a domain fusion that mimics an evolutionary pathway for knotted proteins. Unlike a previously studied knotted protein of similar length, we see reversible folding/knotting and a surprising lack of deep topological traps with a coarse-grained structure-based model. Our main interest is to investigate how evolution might further select the geometry and stiffness of the threading region of the newly fused protein. We compare the folding of the wild-type protein to several mutants. Similarly to the wild-type protein, all mutants show robust and reversible folding, and knotting coincides with the transition state ensemble. As observed experimentally, our simulations show that the knotted protein folds about ten times slower than an unknotted construct with an identical contact map. Simulated folding kinetics reflect the experimentally observed rollover in the folding limbs of chevron plots. Successful folding of the knotted protein is restricted to a narrow range of temperature as compared to the unknotted protein and fits of the kinetic folding data below folding temperature suggest slow, nondiffusive dynamics for the knotted protein.
最近的实验已经确凿地证明，蛋白质能够在没有伴侣蛋白帮助的情况下，从无扭结的变性多肽折叠成扭结的天然状态。这些实验与越来越多的理论工作一致，这些理论工作表明，一个有漏斗形的、最小受挫的能量景观足以折叠具有复杂拓扑结构的小蛋白质。在这里，我们对一种经过实验室工程设计的扭结蛋白 2ouf 的折叠进行了理论研究，该蛋白通过结构域融合模拟了扭结蛋白的进化途径。与之前研究过的类似长度的扭结蛋白不同，我们在一个基于粗粒化结构的模型中看到了可逆折叠/扭结，以及令人惊讶的缺乏深度拓扑陷阱。我们的主要兴趣是研究进化如何进一步选择新融合蛋白的穿线区域的几何形状和刚度。我们比较了野生型蛋白和几种突变体的折叠情况。与野生型蛋白类似，所有突变体都表现出稳健的、可逆的折叠和扭结与过渡态集合一致。与实验观察到的情况一样，我们的模拟表明，与具有相同接触图的无扭结结构相比，扭结蛋白的折叠速度要慢十倍。模拟折叠动力学反映了 Chevron 图中折叠支的实验观察到的翻转。与无扭结蛋白相比，扭结蛋白的成功折叠受到温度的限制，并且低于折叠温度的动力学折叠数据的拟合表明，扭结蛋白的动力学是缓慢的、非扩散的。
