碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

引用本文: 刘帅, 李书实, 刘冬佳, 王长生. 碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点[J]. 物理化学学报, 2013, 29(12): 2551-2557. doi: 10.3866/PKU.WHXB201310293 shu

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

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

基金项目:
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)

大连市领军人才资助项目

摘要:

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.

关键词:

English

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: 28 November 2013
Fund Project:
国家自然科学基金(21173109)

教育部高等学校博士点基金(20102136110001)

辽宁省优秀人才基金(LR2012037)

大连市领军人才资助项目

Abstract:

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.

Key words:

1. [1]
  
  (1) Hobza, P.; Sponer, J. Chem. Rev. 1999, 99, 3247. doi: 10.1021/cr9800255
  (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(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(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(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(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(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(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(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(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(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(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.(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(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(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(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(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.(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(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.(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(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.(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(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(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(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(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(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(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(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(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(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+(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(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.(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.(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(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(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(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
  (38) Scheiner, S. J. Phys. Chem. B 2006, 110, 18670. doi: 10.1021/jp063225q

扫一扫看文章

计量

PDF下载量: 600
文章访问数: 1166
HTML全文浏览量: 49

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

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

English

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

English

Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

计量

文章相关

通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

CCS Chemistry：颜徐州、鲍哲南：你的皮肤可能是一片SPMs