Investigation of viral DNA packaging using molecular mechanics models
Investigation of viral DNA packaging using molecular mechanics models
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DOI：
10.1016/s0301-4622(02)00197-7
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发表时间：
2002-12-10
影响因子：
3.8
通讯作者：
Harvey, SC
中科院分区：
文献类型：
--
作者：
Arsuaga, J;Tan, RKZ;Harvey, SC
一个简单的分子力学模型已经被用来研究具有二十面体对称性的双链DNA分子在衣壳中的最佳线轴状堆积构象。该模型通过每十个基序(大约DNA双螺旋的一圈)使用一个伪原子来表示一个弹性分段链。能量函数中不同项的力常数被选择来近似已知的物理性质，并使用径向约束将DNA限制在一个球体中，其体积相当于典型的噬菌体衣壳的体积。当DNA填充到球体体积的90%时，同轴缠绕模型获得了最优包装，但当空隙体积较大时，这一结果不成立。当球形体积中只有60%充满DNA时，最低能量结构有两层，卷曲的核心与外部同轴缠绕的外壳成一定角度填充。在100%同轴假脱机的模型中，这缓解了与两极附近紧曲率相关的弯曲应变。有趣的是，这些模型的超螺旋密度与细菌细胞中观察到的质粒中的典型数值非常相似。并对该方法的应用前景进行了讨论。(C)2002 Elsevier Science B.V.保留所有权利。
A simple molecular mechanics model has been used to investigate optimal spool-like packing conformations of double-stranded DNA molecules in viral capsids with icosahedral symmetry. The model represents an elastic segmented chain by using one pseudoatom for each ten basepairs (roughly one turn of the DNA double helix). Force constants for the various terms in the energy function were chosen to approximate known physical properties, and a radial restraint was used to confine the DNA into a sphere with a volume corresponding to that of a typical bacteriophage capsid. When the DNA fills 90% of the spherical volume, optimal packaging is obtained for coaxially spooled models, but this result does not hold when the void volume is larger. When only 60% of the spherical volume is filled with DNA, the lowest energy structure has two layers, with a coiled core packed at an angle to an outer coaxially spooled shell. This relieves bending strain associated with tight curvature near the poles in a model with 100% coaxial spooling. Interestingly, the supercoiling density of these models is very similar to typical values observed in plasmids in bacterial cells. Potential applications of the methodology are also discussed. (C) 2002 Elsevier Science B.V. All rights reserved.