Real-time atomistic description of DNA unfolding.
Real-time atomistic description of DNA unfolding.
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DOI：
10.1002/anie.201000593
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发表时间：
2010-06
影响因子：
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通讯作者：
Alberto Pérez;M. Orozco
中科院分区：
文献类型：
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作者：
Alberto Pérez;M. Orozco
尽管最近做出了努力，但DNA的折叠/展开(被理解为在很大一部分双链中从天然构象发生戏剧性的构象变化)仍然描述得很少。一系列经典物理研究导致假设短DNA片段的展开是可逆的，并遵循从d(A·T)对开始的两态机制。[1-3]然而，这一传统观点最近受到超快技术的挑战[4-9]，它提出了一个更复杂的场景，即在微秒长的展开过程中检测到致密的中间产物。[4]不幸的是，这些实验不能提供关于该过程的原子细节信息，因此需要使用模拟技术(主要是分子动力学，MD)作为补充工具。由于计算原因，MD对展开的模拟通常遵循间接方法，例如在非物理变性条件下(T=400K)使用多个短轨迹、[10，11]副本交换、[12，13]或中等大(100 Ns)模拟。[14，15]这些模拟提供了DNA展开的复杂性的明确证据，但无法定义机械观点，这将需要多个非常大的无偏轨迹。在这里，我们给出了一个完整的原子论描述[16]，描述了DNA在真实变性条件下的完整展开。这项研究是MD的一次真正的“环游”，首次提供了DNA在微秒时间尺度上展开的详细原子图像。所有模拟都使用Dickerson S[17](DDD；蛋白质数据库代码1BNA)进行，这是一个研究得很好的短非发夹双链模型。为了确保在微秒时间尺度上展开，[10，11]我们通过添加高浓度的化学变性剂(吡啶；PYR)并将温度提高到接近水的沸点(这些模拟被编码为PHT)来模拟强烈(但现实的)变性条件。进行了控制模拟，考虑了：1)低温下的水(WLT)，我们预计不会
Despite recent efforts, the folding/unfolding of DNA (understood as a dramatic conformational change from the native conformation in a significantly large portion of the duplex) is still poorly described. A range of classical physical studies led to the assumption that the unfolding of short DNA fragments is reversible and follows a two-state mechanism, starting at d (A· T) pairs.[1–3] Nevertheless, this traditional view has been recently challenged [4–9] by ultrafast techniques, which suggested a more complex scenario where compact intermediates are detected during the microsecond-long unfolding process.[4] Unfortunately, these experiments were not able to provide atomistic-detailed information on the process, thus making necessary the use of simulation techniques (mainly molecular dynamics, MD) as complementary tools. For computational reasons MD simulations of unfolding have typically followed indirect approaches, such as the use of multiple short trajectories,[10, 11] replica exchange,[12, 13] or moderately large (100ns) simulations under nonphysical denaturing conditions (T= 400 K).[14, 15] These simulations provided clear evidence of the complexity of DNA unfolding but were unable to define a mechanistic view, which would require multiple very large unbiased trajectories. Herein, we present a full atomistic description [16] of the unfolding of a full turn of DNA under realistic denaturing conditions. The study, a real “tour de force” for MD, provides for the first time a detailed atomistic picture of DNA unfolding in the microsecond timescale.All simulations were performed using Dickerson s dodecamer [17](DDD; Protein Data Bank (PDB) code 1BNA), a well-studied model of a short nonhairpin duplex. To guarantee unfolding on the microsecond timescale,[10, 11] we simulated strong (but realistic) denaturing conditions by adding a high concentration of a chemical denaturant (pyridine; Pyr) and increasing the temperature to nearly the boiling point of water (these simulations are coded as PHT). Control simulations were performed that considered: 1) water at low temperature (WLT), where we expected no