Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.
J Phys Condens Matter. 2010 Apr 21;22(15):152101. doi: 10.1088/0953-8984/22/15/152101. Epub 2010 Mar 9.
The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.
采用从头算量子力学/分子力学计算相结合的方法，研究了环境结构对完全溶剂化 DNA-蛋白质复合物中功能区域电子态的影响。计算所用的复合物为转录因子 PU.1 和靶 DNA。溶剂对一些 DNA 碱基分子轨道（MO）能量的影响与蛋白质对 DNA 碱基的屏蔽程度密切相关。在复合物中，PU.1 通过氢键直接识别 DNA 碱基，并诱导 DNA 结构从规范结构发生变化，从而改变 DNA 碱基之间的大小差异。因此，本研究中发现的强相关性是第一个表明 DNA 碱基识别模式与相应 MO 能级之间存在密切定量关系的证据。因此，已经揭示出每个碱基的电子态都受到蛋白质对 DNA 的识别的高度调控和组织。预计其他生物大分子系统也具有类似的调制机制，这表明这一发现为理解生物大分子系统的调控功能提供了一个新的基础。
