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The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin

机译:C末端GB1β-发夹的折叠和折叠机制

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In this work, we shed new light on a much-studied case of β-hairpin folding by means of advanced molecular dynamics simulations. A fully atomistic description of the protein and the solvent molecule is used, together with metadynamics, to accelerate the sampling and estimate free-energy landscapes. This is achieved using the path collective variables approach, which provides an adaptive description of the mechanism under study. We discover that the folding mechanism is a multiscale process where the turn region conformation leads to two different energy pathways that are connected by elongated structures. The former displays a stable 2:4 native-like structure in which an optimal hydrophobic packing and hydrogen bond pattern leads to 8 kcal/mol of stabilization. The latter shows a less-structured 3:5 β-sheet, where hydrogen bonds and hydrophobic packing provide only 2.5 kcal/mol of stability. This perspective is fully consistent with experimental evidence that shows this to be a prototypical two-state folder, while it redefines the nature of the unfolded state.
机译:在这项工作中,我们借助先进的分子动力学模拟,为研究广泛的β-发夹折叠提供了新的思路。蛋白质和溶剂分子的完整原子描述与元动力学一起用于加速采样和估计自由能态势。这是通过使用路径集体变量方法实现的,该方法提供了对所研究机制的自适应描述。我们发现折叠机制是一个多尺度过程,其中转弯区域构象导致两个不同的能量路径,这些能量路径由细长结构连接。前者显示出稳定的2:4自然样结构,其中最佳的疏水堆积和氢键模式可导致8 kcal / mol的稳定度。后者显示出结构较少的3:5β-折叠,其中氢键和疏水堆积仅提供2.5 kcal / mol的稳定性。这种观点与实验证据完全一致,实验证据表明这是典型的两态文件夹,同时重新定义了展开状态的性质。

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