LaMarque Jaclyn C, Le Thuc-Vy L, Harvey Stephen C
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Biopolymers. 2004 Feb 15;73(3):348-55. doi: 10.1002/bip.10529.
DNA packaging in bacteriophage P4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. The model is a discretized version of an elastic continuum model. The DNA is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. Various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 K) produces the optimal packaged structure. This structure is a concentric spool, rather than the coaxial spool that has been commonly accepted for so many years. This geometry, which was originally suggested by Hall and Schellman in 1982 (Biopolymers Vol. 21, pp. 2011-2031), produces a lower overall elastic energy than coaxial spooling.
利用一种分子力学模型对噬菌体P4中的DNA包装进行了研究，该模型采用简化表示，每一圈双螺旋含有一个伪原子。该模型是弹性连续介质模型的离散化版本。将DNA逐段插入模型衣壳中，每插入一段后重新优化结构。研究了各种优化方案，发现极低温度（0.3K）下的分子动力学产生了最佳的包装结构。这种结构是一个同心线轴，而不是多年来一直被普遍接受的同轴线轴。这种几何结构最初由霍尔和谢尔曼于1982年提出（《生物聚合物》第21卷，第2011 - 2031页），其总弹性能比同轴缠绕更低。
