A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties.
A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties.
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DOI：
10.1063/1.1869417
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发表时间：
2005-03
期刊：
影响因子：
--
通讯作者：
H. Tepper;G. Voth
中科院分区：
文献类型：
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作者：
H. Tepper;G. Voth
提出了一种新的双螺旋分子溶液简化粗粒模型。与脂质双层和胶束的这种模型一样，描述的水平是颗粒和介观的。该模型的颗粒（珠和弹簧）的性质，使一个简单的实施标准的分子动力学模拟代码，并允许调查的热机械性能，而不预先施加任何（形式的）响应函数。介观层次的描述-原子团凝聚成粗粒度的珠子-导致长距离相互作用被有效地筛选，这大大提高了模拟的效率和可扩展性。在不施加局部或全局序参数的情况下，模型分子的线性初始构型自发地组装成双螺旋，这是由于三种贡献之间的相互作用：碱基对、主链和溶剂之间的疏水/亲水相互作用;沿着主链的磷酸盐-磷酸盐排斥;以及有利的碱基对堆积能。我们目前的螺旋形成的过程中，以及为最终状态的平衡特性的结果，并调查如何都依赖于输入参数。目前的模型有希望两条路线的调查：第一，在一组有限的通用参数，局部（原子尺度）扰动对整体螺旋性能的影响可以系统地研究。其次，由于效率允许直接模拟小型和大型（>100个碱基对）系统，该模型为系统粗粒度方法提供了一个试验场。
A new reductionist coarse-grained model is presented for double-helix molecules in solution. As with such models for lipid bilayers and micelles, the level of description is both particulate and mesoscopic. The particulate (bead-and-spring) nature of the model makes for a simple implementation in standard molecular dynamics simulation codes and allows for investigation of thermomechanic properties without preimposing any (form of) response function. The mesoscopic level of description--where groups of atoms are condensed into coarse-grained beads--causes long-range interactions to be effectively screened, which greatly enhances the efficiency and scalability of simulations. Without imposing local or global order parameters, a linear initial configuration of the model molecule spontaneously assembles into a double helix due to the interplay between three contributions: hydrophobic/hydrophilic interactions between base pairs, backbone, and solvent; phosphate-phosphate repulsion along the backbone; and favorable base-pair stacking energy. We present results for the process of helix formation as well as for the equilibrium properties of the final state, and investigate how both depend on the input parameters. The current model holds promise for two routes of investigation: First, within a limited set of generic parameters, the effect of local (atomic-scale) perturbations on overall helical properties can be systematically studied. Second, since the efficiency allows for a direct simulation of both small and large (>100 base pairs) systems, the model presents a testground for systematic coarse-graining methods.