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
1. [1]
  
  (1) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247. doi: 10.1021/cr9800255
2. [2]
  (2) Kennedy, R. J.; Tsang, K. Y.; Kemp, D. S. J. Am. Chem. Soc.2002, 124, 934. doi: 10.1021/ja016285c
3. [3]
  (3) Jones, S.; Heyningen, P.; Berman, H. M.; Thornton, J. M. J. Mol. Biol. 1999, 287, 877. doi: 10.1006/jmbi.1999.2659
4. [4]
  (4) Mukherjee, S.; Majumdar, M.; Bhattacharyya, D. J. Phys. Chem. B 2005, 109, 10484. doi: 10.1021/jp0446231
5. [5]
  (5) Gu, J.;Wang, J.; Leszczynski, J. J. Phys. Chem. B 2006, 110,13590. doi: 10.1021/jp061360x
6. [6]
  (6) Cheng, A. C.; Chen,W.W.; Fuhrmann, C. N.; Frankel, A. D. J. Mol. Biol. 2003, 327, 781. doi: 10.1016/S0022-2836(03)00091-3
7. [7]
  (7) Allers, J.; Shamoo, Y. J. Mol. Biol. 2001, 311, 75. doi: 10.1006/jmbi.2001.4857
8. [8]
  (8) Rutledge, L. R.; Campbell-Verduyn, L. S.; Hunter, K. C.;Wetmore, S. D. J. Phys. Chem. B 2006, 110, 19652. doi: 10.1021/jp061939v
9. [9]
  (9) Ma, G. Z.; Qiu, Y. F.; Nan, J. M.; Xiao, X. Acta Phys. -Chim. Sin. 2008, 24, 1917. [马国正, 求亚芳, 南俊民, 肖信. 物理化学学报, 2008, 24, 1917.] doi: 10.3866/PKU.WHXB20081031
10. [10]
  (10) Fan, D.; Liu, Z. M.; Jin, H.W.; Zhang, L. R. Acta Phys. -Chim. Sin. 2011, 27, 1223. [樊迪, 刘振明, 金宏威, 张亮仁. 物理化学学报, 2011, 27, 1223.] doi: 10.3866/PKU.WHXB20110439
11. [11]
  (11) Schyman, P.; Danielsson, J.; Pinak, M.; Laaksonen, A. J. Phys. Chem. A 2005, 109, 1713. doi: 10.1021/jp045686m
12. [12]
  (12) Rutledge, L. R.; Churchill, C. D. M.;Wetmore, S. D. J. Phys. Chem. B 2010, 114, 3355.
13. [13]
  (13) Leavens, F. M. V.; Churchill, C. D. M.;Wang, S.;Wetmore, S.D. J. Phys. Chem. B 2011, 115, 10990. doi: 10.1021/jp205424z
14. [14]
  (14) Chocholousova, J.; Feig, M. J. Phys. Chem. B 2006, 110,17240. doi: 10.1021/jp0627675
15. [15]
  (15) Qin, S.; Zhou, H. X. J. Phys. Chem. B 2008, 112, 5955. doi: 10.1021/jp075919k
16. [16]
  (16) Rozas, I.; Alkorta, I.; Elguero, J. J. Phys. Chem. B 2004, 108,3335. doi: 10.1021/jp036901m
17. [17]
  (17) Xu, B.; Schones, D. E.;Wang, Y.; Liang, H.; Li, G. PLoS ONE2013, 8, e52460.
18. [18]
  (18) Zhang, Y.; Shen, H.; Zhang, M.; Li, G. J. Phys. Chem. B 2013,117, 982. doi: 10.1021/jp309682t
19. [19]
  (19) Shen, H.; Sun, H.; Li, G. PLoS Comput. Biol. 2010, 8, e1002851.
20. [20]
  (20) Galetich, I.; Stepanian, S. J.; Shelkovsky, V.; Kosevich, M.;Bla i, Y. P.; Adamowicz, L. J. Phys. Chem. A 2000, 104,8965. doi: 10.1021/jp000755s
21. [21]
  (21) Alkorta, I.; Elguero, J. J. Phys. Chem. B 2003, 107, 5306.
22. [22]
  (22) Lee, J.; Kim, J. S.; Seok, C. J. Phys. Chem. B 2010, 114,7662. doi: 10.1021/jp1017289
23. [23]
  (23) Rutledge, L. R.; Navarro-Whyte, L.; Peterson, T. L.;Wetmore,S. D. J. Phys. Chem. A 2011, 115, 12646. doi: 10.1021/jp203248j
24. [24]
  (24) Liu, D. J.;Wang, C. S. Acta Phys. -Chim. Sin. 2012, 28, 2809.[刘冬佳, 王长生. 物理化学学报, 2012, 28, 2809.] doi: 10.3866/PKU.WHXB201209263
25. [25]
  (25) Li, Y.;Wang, C. S. Sci. China. Chem. 2011, 54, 1759. doi: 10.1007/s11426-011-4411-y
26. [26]
  (26) Li,Y.; Jiang, X. N.;Wang, C. S. J. Comput. Chem. 2011, 32,953. doi: 10.1002/jcc.v32.5
27. [27]
  (27) Li,Y.;Wang, C. S. J. Comput. Chem. 2011, 32, 2765. doi: 10.1002/jcc.v32.13
28. [28]
  (28) Huang, C. Y.; Li, Y.;Wang, C. S. Sci. China. Chem. 2013, 56,238. doi: 10.1007/s11426-012-4715-6
29. [29]
  (29) Wang, C. S.; Liu, P.; Yu, N. Acta Phys. -Chim. Sin. 2013, 29,1173. [王长生, 刘朋, 于楠. 物理化学学报, 2013, 29,1173.] doi: 10.3866/PKU.WHXB201303153
30. [30]
  (30) Radoszkowicz, L.; Huppert, D.; Nachliel, E.; Gutman, M. J. Phys. Chem. A 2010, 114, 1017. doi: 10.1021/jp908766e
31. [31]
  (31) Bhattacharyya, S.; Stankovich, M. T.; Truhlar, D. G.; Gao, J. L.J. Phys. Chem. A 2007, 111, 5729. doi: 10.1021/jp071526+
32. [32]
  (32) Kuppuraj, G.; Sargsyan, K.; Hua, Y. H.; Merrill, A. R.; Lim, C.J. Phys. Chem. B 2011, 115, 7932. doi: 10.1021/jp1118663
33. [33]
  (33) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03,Revision D.01; Gaussian Inc.:Wallingford, CT, 2004.
34. [34]
  (34) Biegler, K. F.; Schonbohm, J.; Bayles, D. J. Comput. Chem.2001, 22, 545.
35. [35]
  (35) Zhao, G. J.; Han, K. L. Accounts Chem. Res. 2012, 45, 404. doi: 10.1021/ar200135h
36. [36]
  (36) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B2007, 111, 8940. doi: 10.1021/jp0734530
37. [37]
  (37) Scheiner, S. J. Phys. Chem. B 2005, 109, 16132. doi: 10.1021/jp053416d
38. [38]
  (38) Scheiner, S. J. Phys. Chem. B 2006, 110, 18670. doi: 10.1021/jp063225q
1. [1]
  Huiying Xu , Minghui Liang , Zhi Zhou , Hui Gao , Wei Yi . Application of Quantum Chemistry Computation and Visual Analysis in Teaching of Weak Interactions. University Chemistry, 2025, 40(3): 199-205. doi: 10.12461/PKU.DXHX202407011
2. [2]
  Meijin Li , Xirong Fu , Xue Zheng , Yuhan Liu , Bao Li . The Marvel of NAD⁺: Nicotinamide Adenine Dinucleotide. University Chemistry, 2024, 39(9): 35-39. doi: 10.12461/PKU.DXHX202401027
3. [3]
  Yinglian LI , Chengcheng ZHANG , Xinyu ZHANG , Xinyi WANG . Spin crossover in [Co(pytpy)₂]²⁺ complexes modified by organosulfonate anions. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1162-1172. doi: 10.11862/CJIC.20240087
4. [4]
  Meiyu Lin , Yuxin Fang , Songzhang Shen , Yaqian Duan , Wenyi Liang , Chi Zhang , Juan Su . Exploration and Implementation of a Dual-Pathway Blended Teaching Model in General Chemistry Experiment Course: A Case Study of Copper Glycine Synthesis and Its Thermal Analysis. University Chemistry, 2024, 39(8): 48-53. doi: 10.3866/PKU.DXHX202312042
5. [5]
  Lirui Shen , Kun Liu , Ying Yang , Dongwan Li , Wengui Chang . Synthesis and Application of Decanedioic Acid-N-Hydroxysuccinimide Ester: Exploration of Teaching Reform in Comprehensive Applied Chemistry Experiment. University Chemistry, 2024, 39(8): 212-220. doi: 10.3866/PKU.DXHX202312035
6. [6]
  Feiyang Liu , Liuhong Song , Miaoyu Fu , Zhi Zheng , Gang Xie , Junlong Zhao . Tryptophan’s Employment Journey. University Chemistry, 2024, 39(9): 16-21. doi: 10.12461/PKU.DXHX202404037
7. [7]
  Yanglin Jiang , Mingqing Chen , Min Liang , Yige Yao , Yan Zhang , Peng Wang , Jianping Zhang . Experimental and Theoretical Investigations of Solvent Polarity Effect on ESIPT Mechanism in 4′-N,N-diethylamino-3-hydroxybenzoflavone. Acta Physico-Chimica Sinica, 2025, 41(2): 100012-. doi: 10.3866/PKU.WHXB202309027
8. [8]
  Hong CAI , Jiewen WU , Jingyun LI , Lixian CHEN , Siqi XIAO , Dan LI . Synthesis of a zinc-cobalt bimetallic adenine metal-organic framework for the recognition of sulfur-containing amino acids. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 114-122. doi: 10.11862/CJIC.20240382
9. [9]
  Hong Lu , Yidie Zhai , Xingxing Cheng , Yujia Gao , Qing Wei , Hao Wei . Advancements and Expansions in the Proline-Catalyzed Asymmetric Aldol Reaction. University Chemistry, 2024, 39(5): 154-162. doi: 10.3866/PKU.DXHX202310074
10. [10]
  Yikai Wang , Xiaolin Jiang , Haoming Song , Nan Wei , Yifan Wang , Xinjun Xu , Cuihong Li , Hao Lu , Yahui Liu , Zhishan Bo . 氰基修饰的苝二酰亚胺衍生物作为膜厚不敏感型阴极界面材料用于高效有机太阳能电池. Acta Physico-Chimica Sinica, 2025, 41(3): 2406007-. doi: 10.3866/PKU.WHXB202406007
11. [11]
  Wei HE , Jing XI , Tianpei HE , Na CHEN , Quan YUAN . Application of solar-driven inorganic semiconductor-microbe hybrids in carbon dioxide fixation and biomanufacturing. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 35-44. doi: 10.11862/CJIC.20240364
12. [12]
  Min LIU , Huapeng RUAN , Zhongtao FENG , Xue DONG , Haiyan CUI , Xinping WANG . Neutral boron-containing radical dimers. Chinese Journal of Inorganic Chemistry, 2025, 41(1): 123-130. doi: 10.11862/CJIC.20240362
13. [13]
  Xiaofeng Xia , Jielian Zhu . Innovative Comprehensive Experimental Design: Synthesis of 6-Fluoro-N-benzoyl Tetrahydroquinoline. University Chemistry, 2024, 39(10): 344-352. doi: 10.12461/PKU.DXHX202405063
14. [14]
  Xiaoling LUO , Pintian ZOU , Xiaoyan WANG , Zheng LIU , Xiangfei KONG , Qun TANG , Sheng WANG . Synthesis, crystal structures, and properties of lanthanide metal-organic frameworks based on 2, 5-dibromoterephthalic acid ligand. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1143-1150. doi: 10.11862/CJIC.20230271
15. [15]
  Junjun Huang , Ran Chen , Yajian Huang , Hang Zhang , Anran Zheng , Qing Xiao , Dan Wu , Ruxia Duan , Zhi Zhou , Fei He , Wei Yi . Discovery of an enantiopure N-[2-hydroxy-3-phenyl piperazine propyl]-aromatic carboxamide derivative as highly selective α_1D/1A-adrenoceptor antagonist and homology modelling. Chinese Chemical Letters, 2024, 35(11): 109594-. doi: 10.1016/j.cclet.2024.109594
16. [16]
  Juntao Yan , Liang Wei . 2D S-Scheme Heterojunction Photocatalyst. Acta Physico-Chimica Sinica, 2024, 40(10): 2312024-. doi: 10.3866/PKU.WHXB202312024
17. [17]
  Xiuyun Wang , Jiashuo Cheng , Yiming Wang , Haoyu Wu , Yan Su , Yuzhuo Gao , Xiaoyu Liu , Mingyu Zhao , Chunyan Wang , Miao Cui , Wenfeng Jiang . Improvement of Sodium Ferric Ethylenediaminetetraacetate (NaFeEDTA) Iron Supplement Preparation Experiment. University Chemistry, 2024, 39(2): 340-346. doi: 10.3866/PKU.DXHX202308067
18. [18]
  Jianfeng Yan , Yating Xiao , Xin Zuo , Caixia Lin , Yaofeng Yuan . Comprehensive Chemistry Experimental Design of Ferrocenylphenyl Derivatives. University Chemistry, 2024, 39(4): 329-337. doi: 10.3866/PKU.DXHX202310005
19. [19]
  Liangzhen Hu , Li Ni , Ziyi Liu , Xiaohui Zhang , Bo Qin , Yan Xiong . A Green Chemistry Experiment on Electrochemical Synthesis of Benzophenone. University Chemistry, 2024, 39(6): 350-356. doi: 10.3866/PKU.DXHX202312001
20. [20]
  Zhanhong Tong , Xiaoyu Xie , Fangfang Chen . Appreciating Autumn Leaves: A Brief Analysis of the Causes behind “Frost Leaves Redder than February Flowers”. University Chemistry, 2024, 39(9): 183-188. doi: 10.12461/PKU.DXHX202404005

Get Citation

PDF

XML

Metrics

PDF Downloads(600)
Abstract views(791)
HTML views(21)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142