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首页> 外文会议>NATO Advanced Study Institute on Metal-Ligand Interactions: Molecular, Nano-, Micro-, and Macro-Systems in Complex Environments; 20020901-20020912; Cetraro; IT >Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice
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Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice

机译：微观DNA波动与宏观DNA拉伸弹性一致，而对力场选择的依赖性不强

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Abstract. Multiscale modeling requires the use of information at small length and time scales to parameterize less detailed models at large scales/ We present analysis of molecular dynamics simulation of the solvated double-stranded DNA decamer d(C_5T_s)·(A_5G_5) to parameterize an elastic rod model of DNA. We show that thermal fluctuation of rise along the helix implies stretching elasticity in accord with the macroscopic stretching elasticity observed in single- molecule stretching experiments. We find consistent results from three different force-fields (AMBER, CHARMM and CHARMM-27). Notably, while the base-pair rise averages about 3 A, it fluctuates between 2 and 4 A, i.e. by +- 30%. The lifetime of these fluctuations is roughly one nanosecond. We discuss how these strong thermal deformations may play a role in the binding dynamics of proteins and drugs that deform double helix structure.
机译：抽象。多尺度建模需要使用较小长度和时间尺度的信息来对较不详细的模型进行大规模参数化/我们目前对溶剂化双链DNA decamer d（C_5T_s）·（A_5G_5）的分子动力学模拟进行分析以对弹性杆进行参数化DNA的模型。我们表明，沿螺旋线上升的热波动意味着拉伸弹性与在单分子拉伸实验中观察到的宏观拉伸弹性一致。我们从三个不同的力场（AMBER，CHARMM和CHARMM-27）找到一致的结果。值得注意的是，虽然碱基对平均上升约3 A，但它在2-4 A之间波动，即±30％。这些波动的寿命约为一纳秒。我们讨论了这些强烈的热变形如何在使双螺旋结构变形的蛋白质和药物的结合动力学中发挥作用。

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