Dixit S B, Jayaram B
Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi.
J Biomol Struct Dyn. 1998 Oct;16(2):237-42. doi: 10.1080/07391102.1998.10508242.
Hydrogen bonds have been accredited with a major role historically, in the formation and stabilization of biomolecular structures. The formation of hydrogen bonds at protein-DNA interfaces in aqueous medium involves not only favorable interactions of the donor and acceptor functional groups but also a loss of interactions between these groups with the solvent water. We have investigated the energetics of about 500 potential hydrogen bonds occuring at protein-DNA interfaces incorporating some recent improvements in biomolecular force fields and solvation treatments. We present here results of our assessment of hydrogen bond contributions to the overall standard free energy of formation of protein-DNA complexes obtained with the generalized Born model and finite difference Poisson-Boltzmann methodology for solvation in conjunction with AMBER force field. Our results support the emerging view on the role of electrostatics in general and that of hydrogen bonds in particular which is that hydrogen bonds do not drive protein-DNA complex formation by virtue of the unfavourable cost of the electrostatics of desolvation. They however, act to stabilize the complex once it is formed.
历史上，氢键在生物分子结构的形成和稳定中被认为起着重要作用。在水介质中蛋白质 - DNA 界面处氢键的形成不仅涉及供体和受体官能团的有利相互作用，还涉及这些基团与溶剂水之间相互作用的丧失。我们研究了在蛋白质 - DNA 界面处出现的约 500 个潜在氢键的能量学，其中纳入了生物分子力场和溶剂化处理方面的一些最新改进。在此，我们展示了通过广义玻恩模型和有限差分泊松 - 玻尔兹曼方法结合 AMBER 力场对溶剂化进行评估后，氢键对蛋白质 - DNA 复合物形成的整体标准自由能贡献的评估结果。我们的结果支持了关于静电作用尤其是氢键作用的新观点，即氢键并非凭借去溶剂化静电作用的不利代价来驱动蛋白质 - DNA 复合物的形成。然而，一旦复合物形成，它们会起到稳定复合物的作用。
