鸟嘌呤与氨基酸残基体系的极化力场

doi:10.7503/cjcu20180653

摘要/Abstract

摘要：

发展了应用于鸟嘌呤G和氨基酸残基体系的浮动电荷力场, 该力场明确定义了孤对电子和键的电荷和位置, 通过电荷随着环境的浮动来体现极化效应; 通过氢键拟合函数k_HB描绘了氢键键能. 应用量子化学方法, 对G与氨基酸残基体系从氢键、几何结构及电荷分布3个方面展开计算及分析, 并以其为基准, 确定参数发展了适用于G与氨基酸残基氢键体系的ABEEMσπ PFF. 采用3种不同力场模拟目标分子的结构和性质. 模拟结果表明, 发展的ABEEMσπ PFF与量子化学方法具有最好的一致性, 可用于模拟生物大分子体系.

关键词: 极化力场, 氢键, 碱基, 氨基酸残基

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

中图分类号:

O641

TrendMD:

许炎, 刘翠, 韩成娟, 潘明玉, 孙照琦, 韩冰玉, 杨忠志. 鸟嘌呤与氨基酸残基体系的极化力场. 高等学校化学学报, 2019, 40(2): 288.

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^†. Chem. J. Chinese Universities, 2019, 40(2): 288.

图/表 16

参考文献 27

[1]	Douki T., Berger M., Raoul S., Ravanat J.L., Cadet J., Determination of 8-Oxo-Purines in DNA by HPLC Using Amperometric Detection., Birkhäuser Press, Basel, 1995, 213-224
[2]	Manas E. S., Getahun Z., Wright W. W., DeGradoW. F., Vanderkooi J. M., J. Am. Chem. Soc.,2000, 122(41), 9883-9890
[3]	Shukla A., Barbiellini B., Buslaps T., Suortti P. Z., Phys. Chem.,2001, 215(10), 1315-1321
[4]	Cadet J., Douki T., Ravanat J. L., Photochem. Photobio.,2015, 91(1), 140-155
[5]	Huo H. J., Zhao D. X., Yang Z. Z., Chem. J. Chinese Universities,2011, 32(12), 2877-2884
	(霍红杰, 赵东霞, 杨忠志. 高等学校化学学报, 2011, 32(12), 2877-2884)
[6]	Liu C., Zhang Q. H., Gong L. D., Lu L. N., Yang Z. Z., Chem. J. Chinese Universities,2014, 35(12), 2645-2653
	(刘翠, 张千慧, 宫利东, 卢丽男, 杨忠志. 高等学校化学学报, 2014, 35(12), 2645-2653
[7]	Liu C., Li Y., Han B. Y., Gong L. D., Lu L. N., Yang Z. Z., Zhao D. X., J. Chem. Theory Comput.,2017, 13(5), 2098-2111
[8]	Zhang Q. H., Wang Y., Liu C., Yang Z. Z., Acta Chim. Sinica,2014, 72(8), 956-962
	(张千慧, 王阳, 刘翠, 杨忠志. 化学学报, 2014, 72(8), 956-962)
[9]	Liu S., Li S. S., Liu D. J., Wang C. S., Acta Phys. Chim. Sin., 2013, 29(12), 2551-2557
	(刘硕, 李书实, 刘冬佳, 王长生. 物理化学学报, 2013, 29(12), 2551-2557)
[10]	Wang C. S., Liu P., Yu N., Acta Phys. Chim. Sin., 2013, 29(6), 1173-1182
	(王长生, 刘朋, 于楠. 物理化学学报, 2013, 29(6), 1173-1182)
[11]	González J., Baños I., León I., Contreras-Garcia J., Cocinero E. J., Lesarri A., Fernández J. A., Millán J., J. Chem. Theory Comput., 2016, 12(2), 523-534
[12]	Xie W., Gao J., J. Chem. Theory Comput.,2007, 3(6), 1890-1900
[13]	Wang J., Cieplak P., Li J., Cai Q., Hsieh M., Luo R., Duan Y., J. Phys. Chem. B,2012, 116(24), 7088-7101
[14]	Ivani I., Dans P. D., Noy A., Perez A., Faustino L., Hospital A., Walther J., Andrio P., Goni R., Balaceanu A., Portella G., Battistini F., Gelpi J. L., Gonzalez C., Vendruscolo M., Laughton C. A., Harris S. A., Case D. A., Orozco M., Nat. Methods,2016, 13(1), 55-58
[15]	Kaminski G. A., Stern H. A., Berne B. J., Friesner R. A., Cao Y. X., Murphy R. B., Zhou R., Halgren T. A., J. Comput. Chem., 2002, 23(16), 1515-1531
[16]	Jorgensen W. L., Jensen K. P., Alexandrova A. N., J. Chem. Theory Comput., 2007, 3(6), 1987-1992
[17]	Savelyev A., MacKerell J. A. D., J. Phys. Chem. B,2014, 118(24), 6742-6757
[18]	Lemkul J. A., Huang J., Roux B., Mackerell A. D. Jr., Chem. Rev., 2016, 116(9), 4983-5013
[19]	Zhang C., Bell D., Harger M., Ren P. Y., J. Chem. Theory Comput., 2017, 13(2), 666-678
[20]	Donchev A. G., Ozrin V. D., Subbotin M. V., Tarasov O. V., Tarasov V. I. A., Proc. Natl. Acad. Sci. U. S. A., 2005, 102(22), 7829-7834
[21]	Donchev A. G., Galkin N. G., Illarionov A. A., Khoruzhii O. V., Olevanov M. A., Ozrin V. D., Subbotin M. V., Tarasov V. I., Proc. Natl. Acad. Sci. U. S. A. ,2006, 103(23), 8613-8617
[22]	Zhao D. X., Liu C., Wang F. F., Yu C. Y., Gong L. D., Liu S. B., Yang Z. Z., J. Chem. Theory Comput., 2010, 6(3), 795-804
[23]	Wu Y., Yang Z. Z., J. Phys. Chem. A,2004, 108(37), 7563-7576
[24]	Li X., Yang Z. Z., J. Phys. Chem. A,2005, 109(18), 4102-4111
[25]	Yang Z. Z., Wang J. J., Zhao D. X., J. Comput. Chem., 2014, 35(23), 1690-1706
[26]	Frisch M.J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A., Cheeseman J. R., Scalmani G., Barone V., Mennucci B., Petersson G. A., Nakatsuji H., Caricato M., Li X., Hratchian H. P., Izmaylov A. F., Bloino J., Zheng G., Sonnenberg J. L., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Vreven T., Montgomery J. A., Peralta J. E., Ogliaro F., Bearpark M., Heyd J. J., Brothers E., Kudin K. N., Staroverov V. N., Kobayashi R., Normand J., Raghavachari K., Rendell A., Burant J. C., Iyengar S. S., Tomasi J., Cossi M., Rega N., Millam J. M., Klene M., Knox J. E., Cross J. B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R. E., Yazyev O., Austin A. J., Cammi R., Pomelli C., Ochterski J. W., Martin R. L., Morokuma K., Zakrzewski V. G., Voth G. A., Salvador P., Dannenberg J. J., Dapprich S., Daniels A. D., Farkas O., Foresman J. B., Ortiz J. V., Cioslowski J., Fox D. J., Gaussian 09, Revision A.02, Gaussian Inc., Wallingford CT, 2009
[27]	Hohenstein E. G., Chill S. T., Sherrill C. D., J. Chem. Theory Comput., 2008, 4(12), 1996-2000

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