带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

doi:10.7503/cjcu20160699

摘要/Abstract

摘要：

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.

关键词: 组氨酸侧链, DNA碱基, 离子氢键作用, 堆积作用, T型作用

Abstract:

The gas phase optimal structures of eighteen hydrogen-bonded complexes, composed of a charged histidine side chain and one of DNA bases, were obtained at the MP2/6-31+G(d,p) level, and the corresponding optimal structures in water solvent were obtained at the MP2/6-31+G(d,p) level with the Polarizable Continuum model(PCM). Twelve π-π⁺ stacking and T-shaped complexes composed of a charged histidine side chain and a DNA base were taken from the Wetmore’s work. The gas phase binding energies were evaluated at the CP-corrected MP2/aug-cc-pVTZ and M06-2X-D3/aug-cc-pVDZ level. The binding energies in water solvent were evaluated at the MP2/aug-cc-pVTZ and M06-2X-D3/aug-cc-pVDZ level with the PCM model. Calculation results show that the CP-corrected M06-2X-D3/aug-cc-pVDZ method produces accurate binding energies for these noncovalent complexes. Based on the obtained binding energies, it can be deduced that, in gas phase, the ionic hydrogen bonding is much stronger than the π-π⁺ stacking and T-shaped interaction of a charged histidine with a same base molecule; histidine hydrogen bonds much stronger with either cytosine or guanine than with adenine or thymine; and the π-π⁺ T-shaped interaction of the histidine with guanine or cytosine is stronger than the ionic hydrogen bonding of the histidine with adenine or thymine. In water solvent, the ionic hydrogen bonding between a charged histidine and a same base molecule is still stronger than the π-π⁺ stacking and T-shaped interaction between a charged histidine and a same base molecule; histidine still hydrogen bonds stronger with either cytosine or guanine than with adenine or thymine; but the π-π⁺ T-shaped interaction of the histidine and cytosine is weaker than the ionic hydrogen bonding of the histidine and adenine or thymine; it can be indicated that the charged histidine side chain will mainly interact with DNA bases through ionic hydrogen bond to form hydrogen-bonded complexes in water solvent.

Key words: Histidine side chain, DNA base, Ionic hydrogen bonding, π-π+ Stacking, π-π+ T-shaped interaction

中图分类号:

O641

TrendMD:

李蕾, 李书实, 王长生. 带电组氨酸侧链与DNA碱基间非键作用强度的理论研究. 高等学校化学学报, 2017, 38(1): 56.

LI Lei, LI Shushi, WANG Changsheng. Theoretical Studies on Noncovalent Interactions Between Charged Histidine Side Chain and DNA Base^†. Chem. J. Chinese Universities, 2017, 38(1): 56.

图/表 3

参考文献 37

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Complex	Gas phase				Water solvent
Complex	E_b(g)_CCSD(T)/ (kJ·mol^-1)		E_b(g)_MP2/ (kJ·mol^-1)	E_b(g)_M06/ (kJ·mol^-1)	E_b1(w)_MP2/ (kJ·mol^-1)	E_b1(w)_M06/ (kJ·mol^-1)	E_b2(w)_MP2/ (kJ·mol^-1)
G_His+HB1		-153.80	-153.57		-54.94	-49.24	-52.67
G_His+HB2		-154.76	-153.88		-57.73	-51.41	-55.99
G_His+HB3		-154.77	-154.43		-56.04	-50.13	-53.65
G_His+HB4		-154.71	-153.99		-59.10	-52.87	-57.02
C_His+HB1		-145.98	-146.81		-56.52	-51.69	-56.04
C_His+HB2		-139.75	-141.80		-55.14	-51.12	-54.60
C_His+HB3		-146.90	-147.54		-59.28	-53.63	-58.07
C_His+HB4		-139.32	-141.11		-56.41	-51.91	-54.48
T_His+HB1		-95.65	-93.99		-35.72	-29.62	-37.54
T_His+HB2		-88.24	-86.02		-34.97	-28.96	-36.58
T_His+HB3		-95.98	-94.06		-36.90	-30.76	-40.62
T_His+HB4		-88.20	-85.94		-36.27	-30.25	-38.90
A_His+HB1		-99.62	-96.64		-41.72	-34.97	-43.39
A_His+HB2		-95.40	-94.97		-43.97	-39.46	-44.99
A_His+HB3		-95.48	-90.78		-39.45	-30.48	-43.56
A_His+HB4		-101.42	-97.40		-44.84	-36.86	-45.66
A_His+HB5		-95.40	-94.63		-46.68	-41.67	-47.18
A_His+HB6		-94.93	-89.81		-40.60	-31.18	-42.46
G_His+ST	-68.8	-72.05	-69.12		-25.52	-18.02
C_His+ST	-61.4	-63.09	-61.81		-21.77	-16.96
T_His+ST	-34.8	-38.36	-36.04		-26.26	-20.71
A_His+ST	-54.4	-62.58	-57.47		-39.44	-28.93
G_His+TS1	-108.9	-108.49	-109.36		-22.40	-18.82
G_His+TS2	-85.6	-84.66	-84.86		-22.92	-17.92
C_His+TS1	-97.8	-96.03	-99.45		-23.13	-21.53
C_His+TS2	-88.1	-87.63	-87.34		-26.27	-22.21
T_His+TS1	-54.8	-53.61	-55.08		-13.62	-11.76
T_His+TS2	-51.0	-51.41	-50.71		-21.23	-17.64
A_His+TS1	-43.0	-44.59	-42.37		-16.19	-12.61
A_His+TS2	-63.6	-65.98	-60.16		-26.08	-18.99

Complex	Gas phase				Water solvent
Complex	E_b(g)_CCSD(T)/ (kJ·mol^-1)		E_b(g)_MP2/ (kJ·mol^-1)	E_b(g)_M06/ (kJ·mol^-1)	E_b1(w)_MP2/ (kJ·mol^-1)	E_b1(w)_M06/ (kJ·mol^-1)	E_b2(w)_MP2/ (kJ·mol^-1)
G_His+HB1		-153.80	-153.57		-54.94	-49.24	-52.67
G_His+HB2		-154.76	-153.88		-57.73	-51.41	-55.99
G_His+HB3		-154.77	-154.43		-56.04	-50.13	-53.65
G_His+HB4		-154.71	-153.99		-59.10	-52.87	-57.02
C_His+HB1		-145.98	-146.81		-56.52	-51.69	-56.04
C_His+HB2		-139.75	-141.80		-55.14	-51.12	-54.60
C_His+HB3		-146.90	-147.54		-59.28	-53.63	-58.07
C_His+HB4		-139.32	-141.11		-56.41	-51.91	-54.48
T_His+HB1		-95.65	-93.99		-35.72	-29.62	-37.54
T_His+HB2		-88.24	-86.02		-34.97	-28.96	-36.58
T_His+HB3		-95.98	-94.06		-36.90	-30.76	-40.62
T_His+HB4		-88.20	-85.94		-36.27	-30.25	-38.90
A_His+HB1		-99.62	-96.64		-41.72	-34.97	-43.39
A_His+HB2		-95.40	-94.97		-43.97	-39.46	-44.99
A_His+HB3		-95.48	-90.78		-39.45	-30.48	-43.56
A_His+HB4		-101.42	-97.40		-44.84	-36.86	-45.66
A_His+HB5		-95.40	-94.63		-46.68	-41.67	-47.18
A_His+HB6		-94.93	-89.81		-40.60	-31.18	-42.46
G_His+ST	-68.8	-72.05	-69.12		-25.52	-18.02
C_His+ST	-61.4	-63.09	-61.81		-21.77	-16.96
T_His+ST	-34.8	-38.36	-36.04		-26.26	-20.71
A_His+ST	-54.4	-62.58	-57.47		-39.44	-28.93
G_His+TS1	-108.9	-108.49	-109.36		-22.40	-18.82
G_His+TS2	-85.6	-84.66	-84.86		-22.92	-17.92
C_His+TS1	-97.8	-96.03	-99.45		-23.13	-21.53
C_His+TS2	-88.1	-87.63	-87.34		-26.27	-22.21
T_His+TS1	-54.8	-53.61	-55.08		-13.62	-11.76
T_His+TS2	-51.0	-51.41	-50.71		-21.23	-17.64
A_His+TS1	-43.0	-44.59	-42.37		-16.19	-12.61
A_His+TS2	-63.6	-65.98	-60.16		-26.08	-18.99