de Sancho David, Best Robert B
CIC nanoGUNE , 20018 Donostia-San Sebastián, Spain.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States.
J Phys Chem Lett. 2016 Oct 6;7(19):3798-3803. doi: 10.1021/acs.jpclett.6b01722. Epub 2016 Sep 14.
Most experimentally well-characterized single domain proteins of less than 100 residues have been found to be two-state folders. That is, only two distinct populations can explain both equilibrium and kinetic measurements. Results from single molecule force spectroscopy, where a protein is unfolded by applying a mechanical pulling force to its ends, have largely confirmed this description for proteins found to be two-state in ensemble experiments. Recently, however, stable intermediates have been reported in mechanical unfolding experiments on a cold-shock protein previously found to be a prototypical two-state folder. Here, we tackle this discrepancy using free energy landscapes and Markov state models derived from coarse-grained molecular simulations. We show that protein folding intermediates can be selectively stabilized by the pulling force and that the populations of these intermediates vary in a force-dependent manner. Our model qualitatively captures the experimental results and suggests a possible origin of the apparent discrepancy.
大多数实验特征明确、少于100个残基的单结构域蛋白质已被发现是两态折叠体。也就是说，只有两种不同的群体才能解释平衡和动力学测量结果。单分子力谱实验的结果在很大程度上证实了这一描述，该实验通过对蛋白质两端施加机械拉力使其展开，对于在整体实验中被发现为两态的蛋白质来说。然而，最近在对一种先前被发现是典型两态折叠体的冷休克蛋白进行的机械展开实验中报告了稳定中间体。在这里，我们使用从粗粒度分子模拟得出的自由能景观和马尔可夫状态模型来解决这一差异。我们表明，蛋白质折叠中间体可以被拉力选择性地稳定，并且这些中间体的群体以力依赖的方式变化。我们的模型定性地捕捉了实验结果，并提出了明显差异的可能来源。
