Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States.
J Chem Theory Comput. 2015 Jun 9;11(6):2801-12. doi: 10.1021/acs.jctc.5b00088.
We present an analysis of the most extensive explicit-solvent simulations of β-hairpins to date (9.4 ms in aggregate), with the aim of probing the effects of tryptophan mutations on folding. From molecular simulations of GB1 hairpin, trpzip4, trpzip5, and trpzip6 performed on Folding@home, Markov State Models (MSMs) were constructed using a unified set of metastable states, enabling objective comparison of folding mechanisms. MSM models display quantitative agreement with experimental structural observables and folding kinetics, and predict multimodal kinetics due to specific non-native kinetic traps, which be identified as on- or off-pathway from the network topology. We quantify kinetic frustration by several means, including the s-ensemble method to evaluate glasslike behavior. Free-energy profiles and transition state movement clearly show stabilization of non-native states as Trp mutations are introduced. Remarkably, we find that "β-capped" sequences (trpzip4 and trpzip5) are able to overcome this frustration and remain cooperative two-state folders with a large time-scale gap. These results suggest that, while β-capping motifs are robust, fold stabilization by tryptophan generally may require overcoming significant non-native kinetic traps, perhaps explaining their under-representation in natural proteins.
我们对迄今为止最广泛的β发夹的显溶剂模拟进行了分析（总计 9.4 毫秒），旨在探究色氨酸突变对折叠的影响。通过在 Folding@home 上对 GB1 发夹、trpzip4、trpzip5 和 trpzip6 进行分子模拟，构建了马尔可夫状态模型（MSM），使用统一的亚稳态集，从而能够对折叠机制进行客观比较。MSM 模型与实验结构观测和折叠动力学具有定量一致性，并预测了由于特定的非天然动力学陷阱而导致的多模态动力学，这些动力学陷阱可以通过网络拓扑结构来识别是在途径上还是在途径外。我们通过多种方法来量化动力学受挫，包括 s 集合方法来评估玻璃样行为。自由能曲线和过渡态运动清楚地表明，随着色氨酸突变的引入，非天然状态得到了稳定。值得注意的是，我们发现“β 封端”序列（trpzip4 和 trpzip5）能够克服这种受挫，并保持具有大时间尺度间隔的协同两态折叠体。这些结果表明，虽然β封端基序是稳健的，但色氨酸对折叠的稳定作用通常可能需要克服显著的非天然动力学陷阱，这也许可以解释它们在天然蛋白质中代表性不足的原因。
