Development of Polarization Force Field for Guanine and Amino Acid Residues Systems†

doi:10.7503/cjcu20180653

Abstract

Abstract:

The recognition of DNA depends mainly on the hydrogen bonding between corresponding residues of the enzyme and base. Hydrogen bonding is important for maintaining the stability of DNA and protein structures. In order to more realistically simulate biomolecules, a polarization force field(PFF) has been proposed. The main difference between the different force fields is the handling of electrostatic interactions. A fluctuating charge force field was developed and applied to guanine G and amino acid residue systems. In order to accurately describe the hydrogen bond, the force field clearly defines the charge and position of the lone pair of electrons and bonds. The polarization effect was reflected by the floating of the charge with the environment. The position of the lone pair of electrons has a good control of the angle of hydrogen bonds. The hydrogen bond energy was depicted by the hydrogen bond fitting function k_HB. The quantum chemical method was used to calculate and analyze the G and amino acid residue systems from hydrogen bond, geometry and charge distribution. Based on this, the parameter was confirmed and applied to the hydrogen bond system of G and amino acid residues. Three different force fields were used to simulate the structure and property of target molecules. The simulation results show that the developed ABEEMσπ PFF has the best consistency with the quantum chemical method.

Key words: Polarization force field, Hydrogen bond, Base, Amino acid residue

CLC Number:

O641

TrendMD:

XU Yan,LIU Cui,HAN Chengjuan,PAN Mingyu,SUN Zhaoqi,HAN Bingyu,YANG Zhongzhi. Development of Polarization Force Field for Guanine and Amino Acid Residues Systems^†[J]. Chem. J. Chinese Universities, 2019, 40(2): 288.

Figures/Tables 16

References 27

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Hydrogen bond	k'	C	r_lp_,H	D
lpN307102, H-N101106	0.7010	0.0931	1.3019	0.0319
lpN307102, H-N101109	0.5438	0.0931	1.3019	0.0319
lpN307102, H-N101111	0.5840	0.0931	1.3019	0.0319
lpN307202, H-N101111	0.5744	0.2500	2.0000	0.0500
lpO308102, H-N101116	0.5800	0.0931	1.5019	0.0319
lpO308102, H-N101117	0.5450	0.0931	1.3019	0.0319
lpO308201, H-N101106	0.6000	0.0792	2.0874	0.3202
lpO308201, H-N101116	0.5850	0.0506	1.2523	0.0536
lpO308201, H-N101117	0.6030	0.0931	1.3019	0.0319
lpO308207, H-N101106	0.4800	0.0931	1.3019	0.0319
lpO308207, H-N101111	0.6570	0.0951	1.5019	0.0519
lpS316102, H-N101116	0.8000	0.0931	1.3019	0.0319
lpS316102, H-N101117	0.6400	0.0931	1.3019	0.0319

Hydrogen bond	k'	C	r_lp_,H	D
lpN307102, H-N101106	0.7010	0.0931	1.3019	0.0319
lpN307102, H-N101109	0.5438	0.0931	1.3019	0.0319
lpN307102, H-N101111	0.5840	0.0931	1.3019	0.0319
lpN307202, H-N101111	0.5744	0.2500	2.0000	0.0500
lpO308102, H-N101116	0.5800	0.0931	1.5019	0.0319
lpO308102, H-N101117	0.5450	0.0931	1.3019	0.0319
lpO308201, H-N101106	0.6000	0.0792	2.0874	0.3202
lpO308201, H-N101116	0.5850	0.0506	1.2523	0.0536
lpO308201, H-N101117	0.6030	0.0931	1.3019	0.0319
lpO308207, H-N101106	0.4800	0.0931	1.3019	0.0319
lpO308207, H-N101111	0.6570	0.0951	1.5019	0.0519
lpS316102, H-N101116	0.8000	0.0931	1.3019	0.0319
lpS316102, H-N101117	0.6400	0.0931	1.3019	0.0319

Class	V₂/(kJ·mol^-1)	Class	V₂/(kJ·mol^-1)	Class	V₂/(kJ·mol^-1)
84-71-75-75	6.90	83-71-79-81	5.65	75-73-76-71	41.84
84-71-75-72	6.90	78-72-75-75	17.36	75-73-76-82	41.84
84-71-76-73	7.11	75-72-78-71	20.08	83-74-78-71	10.04
84-71-76-82	7.11	75-72-78-74	20.08	83-74-78-72	10.04
78-71-79-75	5.65	76-73-75-75	10.67	71-75-75-73	22.80
83-71-79-71	5.65	76-73-75-79	6.28	72-75-75-73	22.80

Class	V₂/(kJ·mol^-1)	Class	V₂/(kJ·mol^-1)	Class	V₂/(kJ·mol^-1)
84-71-75-75	6.90	83-71-79-81	5.65	75-73-76-71	41.84
84-71-75-72	6.90	78-72-75-75	17.36	75-73-76-82	41.84
84-71-76-73	7.11	75-72-78-71	20.08	83-74-78-71	10.04
84-71-76-82	7.11	75-72-78-74	20.08	83-74-78-72	10.04
78-71-79-75	5.65	76-73-75-75	10.67	71-75-75-73	22.80
83-71-79-71	5.65	76-73-75-79	6.28	72-75-75-73	22.80

Class	ν/(kJ·mol^-1)	Class	ν/(kJ·mol^-1)	Class	ν/(kJ·mol^-1)	Class	ν/(kJ·mol^-1)
72-75-75-71	41.84	71-72-79-81	41.84	79-78-71-83	41.84	75-75-71-84	41.84
79-75-75-71	41.84	71-75-79-81	41.84	79-79-71-83	41.84	76-75-71-84	41.84
79-75-75-73	41.84	73-71-76-82	41.84	78-83-74-83	87.86	79-75-71-84	41.84
71-71-79-81	41.84	79-75-71-83	41.84