Huang Lulu, Massa Lou, Karle Jerome
Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375-5341, USA.
Biochemistry. 2005 Dec 20;44(50):16747-52. doi: 10.1021/bi051655l.
The kernel energy method (KEM) has been used in three recent papers (1-3) to calculate the quantum mechanical ab inito molecular energy of peptides and the protein insulin. It was found to have good accuracy. The computational difficulty of representing a molecule increases only modestly with the number of atoms. The calculations are simplified by adopting the approximation that a full biological molecule can be represented by smaller "kernels" of atoms. In this paper, the accuracy of the KEM is tested in the application to DNA, whose basic kernels, chemical bonding, and overall molecular structure are quite different from peptides and proteins. The basic kernel in the case of peptides and proteins is an amino acid. The basic kernel in the case of DNA is a nucleotide consisting of a phosphate-sugar-base. The molecular energy is calculated for all three basic types of DNA, i.e., B, A, and Z configurations of DNA. The results give an accuracy that is comparable to that achieved with peptides and proteins. Thus, the KEM is found to be applicable to major types of biological molecules.
内核能量法（KEM）已在最近的三篇论文（1 - 3）中用于计算肽和蛋白质胰岛素的量子力学从头算分子能量。结果发现该方法具有良好的准确性。表示一个分子的计算难度仅随着原子数量的增加而适度增大。通过采用这样一种近似方法简化了计算，即一个完整的生物分子可以由较小的原子“内核”来表示。在本文中，对KEM应用于DNA时的准确性进行了测试，DNA的基本内核、化学键和整体分子结构与肽和蛋白质有很大不同。肽和蛋白质情况下的基本内核是氨基酸。DNA情况下的基本内核是由磷酸 - 糖 - 碱基组成的核苷酸。针对所有三种基本类型的DNA，即DNA的B型、A型和Z型构型计算了分子能量。结果给出的准确性与肽和蛋白质的情况相当。因此，发现KEM适用于主要类型的生物分子。
