van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.
Biophys J. 2010 Feb 17;98(4):646-56. doi: 10.1016/j.bpj.2009.10.039.
We report a numerical study of the (un)folding routes of the truncated FBP28 WW domain at ambient conditions using a combination of four advanced rare event molecular simulation techniques. We explore the free energy landscape of the native state, the unfolded state, and possible intermediates, with replica exchange molecular dynamics. Subsequent application of bias-exchange metadynamics yields three tentative unfolding pathways at room temperature. Using these paths to initiate a transition path sampling simulation reveals the existence of two major folding routes, differing in the formation order of the two main hairpins, and in hydrophobic side-chain interactions. Having established that the hairpin strand separation distances can act as reasonable reaction coordinates, we employ metadynamics to compute the unfolding barriers and find that the barrier with the lowest free energy corresponds with the most likely pathway found by transition path sampling. The unfolding barrier at 300 K is approximately 17 k(B)T approximately 42 kJ/mol, in agreement with the experimental unfolding rate constant. This work shows that combining several powerful simulation techniques provides a more complete understanding of the kinetic mechanism of protein folding.
我们报告了在环境条件下使用四种先进的稀有事件分子模拟技术组合对截断 FBP28 WW 结构域的（去）折叠途径的数值研究。我们使用 replica 交换分子动力学探索了天然状态、展开状态和可能的中间体的自由能景观。随后应用偏置交换元动力学得到了三种在室温下的可能展开途径。使用这些路径来启动转移路径采样模拟揭示了两种主要折叠途径的存在，它们在两个主要发夹的形成顺序以及疏水性侧链相互作用方面有所不同。已经确定发夹链分离距离可以作为合理的反应坐标，我们使用元动力学来计算展开势垒，并发现具有最低自由能的势垒对应于通过转移路径采样发现的最可能途径。在 300 K 时的展开势垒约为 17 k(B)T 约 42 kJ/mol，与实验展开速率常数一致。这项工作表明，结合几种强大的模拟技术可以更全面地了解蛋白质折叠的动力学机制。
