Investigation on the Hydrogen Bonding Interaction Between Amino Acid Side Chains and Base Pairs Containing Oxidized Guanine†

doi:10.7503/cjcu20160952

Abstract

Abstract:

The hydrogen bond energy, geometry, charge distribution and second order stabilization energy of complexes oxidized base pair(8-oxo-G∶C) and Amino acid side chains were investigated via quantum chemistry in gas phase and aqueous solution. The results show that the hydrogen bond strength has been weakened in aqueous solution, the charge has been obviously affected by aqueous solution, the charge variation of forming hydrogen bond sites under aqueous solution is about 10 times as much as under gas phase and the geometry has slight change. Therefore the interaction between enzyme and DNA must be studied in aqueous solution. The aqueous solution has a great influence on the hydrogen bond strength between 8-oxo-G∶C and amino acid side chains in charged complexes, which has been weakened by 69.23 kJ/mol in average. The hydrogen bond strength between 8-oxo-G∶C and amino acid side chains in uncharged complexes has only been weakened by 3.60 kJ/mol in average. The side chain with or without charge has little effect on the hydrogen bond strength between 8-oxo-G and C in complexes in aqueous solution and the hydrogen bond strengths of charged complexes and uncharged complexes have been weakened by 24.57 and 30.05 kJ/mol, respectively. The higher the second-order stabilization energy, the shorter the length of the corresponding hydrogen bonds.

Key words: Complex oxidized base pair(8-oxo-G∶C), Amino acid side chain, Hydrogen bond energy, Natural bond orbital, Quantum chemistry method

CLC Number:

O641

TrendMD:

HAN Bingyu, LI Yue, LIU Cui. Investigation on the Hydrogen Bonding Interaction Between Amino Acid Side Chains and Base Pairs Containing Oxidized Guanine^†[J]. Chem. J. Chinese Universities, 2017, 38(6): 1068.

Figures/Tables 7

References 29

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Geometry	ΔL/nm	Δθ/(°)	ΔL_gas/nm	Δθ_gas/(°)	ΔL_water/nm	Δθ_water/(°)
Region 1	-0.0043—0.0224 (0.0071)	-8.5—5.0(2.0)
Charged complex	0.0079—0.0224 (0.0178)	-2.8—2.0(1.2)
Neutralcomplex	-0.0043—0.0149 (0.0032)	-8.5—5.0(2.3)
Region 2	-0.0143—0.0125 (0.0030)	-2.2—3.1(1.4)	-0.0130—0.0077 (0.0020)	-3.6—2.4(0.9)	-0.0023—0.0036 (0.0001)	-4.5—1.7(0.4)
Charged complex	0.0014—0.0050 (0.0011)	-0.7—2.2(1.5)	-0.0130—0.0077 (0.0061)	-3.4—2.4(1.4)	-0.0023—0.0008 (0.0001)	-0.7—0(0.3)
Neutral complex	-0.0143—0.0125 (0.0037)	-2.2—3.1(1.4)	-0.0046—0.0072 (0.0005)	-3.6—2.4(0.7)	-0.0008—0.0036 (0.0001)	-4.5—1.7(0.4)

Geometry	ΔL/nm	Δθ/(°)	ΔL_gas/nm	Δθ_gas/(°)	ΔL_water/nm	Δθ_water/(°)
Region 1	-0.0043—0.0224 (0.0071)	-8.5—5.0(2.0)
Charged complex	0.0079—0.0224 (0.0178)	-2.8—2.0(1.2)
Neutralcomplex	-0.0043—0.0149 (0.0032)	-8.5—5.0(2.3)
Region 2	-0.0143—0.0125 (0.0030)	-2.2—3.1(1.4)	-0.0130—0.0077 (0.0020)	-3.6—2.4(0.9)	-0.0023—0.0036 (0.0001)	-4.5—1.7(0.4)
Charged complex	0.0014—0.0050 (0.0011)	-0.7—2.2(1.5)	-0.0130—0.0077 (0.0061)	-3.4—2.4(1.4)	-0.0023—0.0008 (0.0001)	-0.7—0(0.3)
Neutral complex	-0.0143—0.0125 (0.0037)	-2.2—3.1(1.4)	-0.0046—0.0072 (0.0005)	-3.6—2.4(0.7)	-0.0008—0.0036 (0.0001)	-4.5—1.7(0.4)

Complex	Charge(OG)/e						Charge(C)/e
Complex	H7	H7'	N9	N9'	O11	O11'	O21	O21'	H23	H23'	H26	H26'
OGC	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.716	-0.735	0.462	0.465	0.459	0.459
OGC1Arg1	0.463	0.456	-0.649	-0.654	-0.707	-0.733	-0.668	-0.721	0.470	0.467	0.468	0.462
OGC1Arg2	0.463	0.456	-0.649	-0.654	-0.707	-0.733	-0.668	-0.721	0.470	0.467	0.469	0.462
OGC7Arg1	0.463	0.456	-0.646	-0.654	-0.695	-0.733	-0.686	-0.727	0.468	0.466	0.465	0.460
OGC7Arg2	0.462	0.456	-0.646	-0.654	-0.695	-0.733	-0.686	-0.727	0.468	0.466	0.465	0.460
OGC2Asn	0.468	0.457	-0.641	-0.654	-0.683	-0.732	-0.713	-0.734	0.464	0.465	0.455	0.454
OGC3Asn	0.468	0.455	-0.636	-0.649	-0.718	-0.743	-0.723	-0.737	0.459	0.463	0.444	0.453
OGC4Asn	0.447	0.447	-0.653	-0.656	-0.702	-0.736	-0.744	-0.744	0.464	0.465	0.460	0.458
OGC5Asn	0.467	0.456	-0.640	-0.654	-0.689	-0.732	-0.753	-0.748	0.461	0.464	0.457	0.459
OGC6Asn	0.469	0.457	-0.640	-0.654	-0.692	-0.733	-0.700	-0.734	0.461	0.464	0.458	0.459
OGC2Ser	0.468	0.456	-0.641	-0.654	-0.688	-0.733	-0.710	-0.730	0.464	0.466	0.458	0.459
OGC5Ser	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.732	-0.730	0.463	0.466	0.459	0.459
OGC6Ser	0.468	0.456	-0.641	-0.654	-0.692	-0.733	-0.707	-0.732	0.462	0.465	0.459	0.459
OGC2Cys	0.466	0.457	-0.641	-0.654	-0.689	-0.733	-0.713	-0.735	0.463	0.465	0.458	0.458
OGC5Cys	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.737	-0.738	0.462	0.465	0.459	0.459
OGC6Cys	0.468	0.457	-0.641	-0.654	-0.692	-0.733	-0.709	-0.734	0.462	0.465	0.459	0.459

Complex	Charge(OG)/e						Charge(C)/e
Complex	H7	H7'	N9	N9'	O11	O11'	O21	O21'	H23	H23'	H26	H26'
OGC	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.716	-0.735	0.462	0.465	0.459	0.459
OGC1Arg1	0.463	0.456	-0.649	-0.654	-0.707	-0.733	-0.668	-0.721	0.470	0.467	0.468	0.462
OGC1Arg2	0.463	0.456	-0.649	-0.654	-0.707	-0.733	-0.668	-0.721	0.470	0.467	0.469	0.462
OGC7Arg1	0.463	0.456	-0.646	-0.654	-0.695	-0.733	-0.686	-0.727	0.468	0.466	0.465	0.460
OGC7Arg2	0.462	0.456	-0.646	-0.654	-0.695	-0.733	-0.686	-0.727	0.468	0.466	0.465	0.460
OGC2Asn	0.468	0.457	-0.641	-0.654	-0.683	-0.732	-0.713	-0.734	0.464	0.465	0.455	0.454
OGC3Asn	0.468	0.455	-0.636	-0.649	-0.718	-0.743	-0.723	-0.737	0.459	0.463	0.444	0.453
OGC4Asn	0.447	0.447	-0.653	-0.656	-0.702	-0.736	-0.744	-0.744	0.464	0.465	0.460	0.458
OGC5Asn	0.467	0.456	-0.640	-0.654	-0.689	-0.732	-0.753	-0.748	0.461	0.464	0.457	0.459
OGC6Asn	0.469	0.457	-0.640	-0.654	-0.692	-0.733	-0.700	-0.734	0.461	0.464	0.458	0.459
OGC2Ser	0.468	0.456	-0.641	-0.654	-0.688	-0.733	-0.710	-0.730	0.464	0.466	0.458	0.459
OGC5Ser	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.732	-0.730	0.463	0.466	0.459	0.459
OGC6Ser	0.468	0.456	-0.641	-0.654	-0.692	-0.733	-0.707	-0.732	0.462	0.465	0.459	0.459
OGC2Cys	0.466	0.457	-0.641	-0.654	-0.689	-0.733	-0.713	-0.735	0.463	0.465	0.458	0.458
OGC5Cys	0.468	0.457	-0.641	-0.654	-0.691	-0.733	-0.737	-0.738	0.462	0.465	0.459	0.459
OGC6Cys	0.468	0.457	-0.641	-0.654	-0.692	-0.733	-0.709	-0.734	0.462	0.465	0.459	0.459