Reich Lothar, Becker Marion, Seckler Robert, Weikl Thomas R
Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany.
Biophys Chem. 2009 May;141(2-3):186-92. doi: 10.1016/j.bpc.2009.01.015. Epub 2009 Feb 12.
Parallel beta-helices are among the simplest repetitive structural elements in proteins. The folding behavior of beta-helix proteins has been studied intensively, also to gain insight on the formation of amyloid fibrils, which share the parallel beta-helix as a central structural motif. An important system for investigating beta-helix folding is the tailspike protein from the Salmonella bacteriophage P22. The central domain of this protein is a right-handed parallel beta-helix with 13 windings. Extensive mutational analyses of the P22 tailspike protein have revealed two main phenotypes: temperature-sensitive-folding (tsf) mutations that reduce the folding efficiency at elevated temperatures, and global suppressor (su) mutations that increase the tailspike folding efficiency. A central question is whether these phenotypes can be understood from changes in the protein stability induced by the mutations. Experimental determination of the protein stability is complicated by the nearly irreversible trimerization of the folded tailspike protein. Here, we present calculations of stability changes with the program FoldX, focusing on a recently published extensive data set of 145 singe-residue alanine mutants. We find that the calculated stability changes are correlated with the experimentally measured invivo folding efficiencies. In addition, we determine the free-energy landscape of the P22 tailspike protein in a nucleation-propagation model to explore the folding mechanism of this protein, and obtain a processive folding route on which the protein nucleates in the N-terminal region of the helix.
平行β-螺旋是蛋白质中最简单的重复结构元件之一。人们对β-螺旋蛋白的折叠行为进行了深入研究，这也是为了深入了解淀粉样纤维的形成，淀粉样纤维也具有平行β-螺旋作为核心结构基序。研究β-螺旋折叠的一个重要体系是来自沙门氏菌噬菌体P22的尾刺蛋白。该蛋白的中央结构域是一个具有13个螺旋圈的右手平行β-螺旋。对P22尾刺蛋白进行的广泛突变分析揭示了两种主要表型：温度敏感折叠（tsf）突变，其在升高温度时会降低折叠效率；以及全局抑制（su）突变，其会提高尾刺蛋白的折叠效率。一个核心问题是，这些表型是否可以从突变引起的蛋白质稳定性变化来理解。由于折叠后的尾刺蛋白几乎不可逆地三聚化，蛋白质稳定性的实验测定变得复杂。在这里，我们使用FoldX程序给出稳定性变化的计算结果，重点关注最近发表的包含145个单残基丙氨酸突变体的大量数据集。我们发现，计算得到的稳定性变化与实验测量的体内折叠效率相关。此外，我们在成核-传播模型中确定了P22尾刺蛋白的自由能景观，以探索该蛋白的折叠机制，并获得了一条渐进式折叠途径，该蛋白在螺旋的N端区域成核。
