Theoretical Studies on Noncovalent Interactions Between Charged Histidine Side Chain and DNA Base†

doi:10.7503/cjcu20160699

Abstract

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

CLC Number:

O641

TrendMD:

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

Figures/Tables 3

References 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