Citation: LIU Shuai, LI Shu-Shi, LIU Dong-Jia, WANG Chang-Sheng. Site Preferences of Adenine Hydrogen Bonding to Peptide Amides[J]. Acta Physico-Chimica Sinica, ;2013, 29(12): 2551-2557. doi: 10.3866/PKU.WHXB201310293 shu

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

1.
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China

Received Date: 11 August 2013
Available Online: 29 October 2013
Fund Project: 国家自然科学基金(21173109) (21173109) 教育部高等学校博士点基金(20102136110001) (20102136110001) 辽宁省优秀人才基金(LR2012037) (LR2012037)

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 hydrogenbonded 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 hydrogenbonded 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.
- Adenine,
- N-methylacetamide,
- Glycine dipeptide,
- Alanine dipeptide,
- Hydrogen bond,
- Binding energy
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