碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计,进而制备具有特殊纳米结构和功能的生物分子材料.本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20个氢键复合物的结构并计算了结合能,探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点.研究发现:腺嘌呤可以使用两个不同位点(A1位点和A2位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物,腺嘌呤使用A1位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定;二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物,二肽分子使用Ala7或Gly7位点与腺嘌呤形成的氢键复合物更稳定;腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用.基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.

A detailed understanding of how nucleobases interact with protein peptides will allow us to gain valuable insights into how these interesting biological molecules could be used to construct complex nanostructures and materials. In this work, the optimal structures and binding energies of 20 hydrogen- bonded complexes, which contained the nucleic acid base adenine, N-methylacetamide, a glycine dipeptide, and an alanine dipeptide, were obtained. The site preferences of adenine hydrogen bonding to peptide amides were explored. The calculation results show that adenine can use two binding sites （site A1 and site A2） to form N--H...N or N--H...O=C hydrogen-bonded complexes with N-methylacetamide; the N--H...N hydrogen-bonded complexes formed at site A1 of adenine are more stable. The calculation results also show that the glycine dipeptide can use either site Gly7 or site Gly5, and the alanine dipeptide can use either site Ala7 or site Ala5 to form hydrogen-bonded complexes with adenine; the hydrogen- bonded complexes formed at site Gly7 of the glycine dipeptide and at site Ala7 of the alanine dipeptide are more stable. The hydrogen-bonded complexes formed by adenine and a dipeptide have larger negative binding energies than the complexes formed by adenine and N-methylacetamide, indicating that the interaction between adenine and the peptide is preferred to that between adenine and N-methylacetamide. The nature of the hydrogen bonding in these complexes was further explored based on the atoms in molecules calculations and the natural bond orbital analysis.