漆酶与酚类模式底物的结合及反应活性的理论研究

doi:10.7503/cjcu20131287

高等学校化学学报 ›› 2014, Vol. 35 ›› Issue (4): 776.doi: 10.7503/cjcu20131287

漆酶与酚类模式底物的结合及反应活性的理论研究

齐艳兵, 朱吉人, 孙尧金, 杜芸, 褚建君, 石婷, 赵一雷(), 王晓雷()

上海交通大学微生物代谢国家重点实验室及生命科学技术学院, 上海 200240

收稿日期:2013-12-27 出版日期:2014-04-10 发布日期:2014-02-25
作者简介:联系人简介: 赵一雷, 男, 博士, 教授, 博士生导师, 主要从事生物分子结构计算和动力学研究. E-mail: yileizhao@sjtu.edu.cn; 王晓雷, 男, 博士后, 主要从事氧化还原酶分子机理研究. E-mail: thundawner@gmail.com;† 现在上海中学工作.
基金资助:
国家“八六三”计划(批准号: 2012AA020403)、国家“九七三”计划(批准号: 2012CB721005, 2013CB966802)、国家自然科学基金(批准号: 21377085, 21303101, 31121064, J1210047)、教育部新世纪优秀人才(批准号: 12-0354)、高等学校博士学科点专项科研基金(批准号: 20100073120062)、教育部留学回国人员科研启动基金、上海市浦江人才计划(批准号: 10 PJ1405200)、 “东方学者”人才计划(批准号: 0900000171)和“上海交通大学-上海中学科技创新项目”资助

Theoretical Studies of the Binding-affinity and Reactivity Between Laccase and Phenolic Substrates^†

QI Yanbing, ZHU Jiren, SUN Yaojin, DU Yun, CHU Jianjun, SHI Ting, ZHAO Yilei^*(), WANG Xiaolei^*()

State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China

Received:2013-12-27 Online:2014-04-10 Published:2014-02-25
Contact: ZHAO Yilei,WANG Xiaolei E-mail:yileizhao@sjtu.edu.cn;thundawner@gmail.com
Supported by:
† Supported by the National High Technology Research and Development Program of China(No.2012AA020403) and the State Key Development Program for Basic Research of China(Nos.2012CB721005, 2013CB966802), National Science Foundation of China(Nos.21377085, 21303101, 31121064, J1210047), New Century Excellent Talents in University of Ministry of Education of China(No.12-0354), Specialized Research Fund for the Doctoral Program of Higher Education of China(No.20100073120062), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, Ministry of Education, China, Shanghai Pujiang Program, China(No.10PJ1405200) and Municipal Education Commission, China(Oriental Professorial Scholarship)(No.0900000171), and Innovation Program of Shanghai High School, China

摘要/Abstract

摘要：

通过生物信息学分析、分子动力学模拟及量子化学计算, 对21种邻对位取代酚类模式底物与漆酶的结合能力以及反应活性进行了探讨. 生物信息学结构比对分析发现漆酶的活性口袋含有Asp/Glu206, Asn/His208, Asn264, Gly392和His458等保守的氨基酸残基(氨基酸残基编号以Trametes versicolor漆酶为例, PDB: 1KYA); 采用MM-GBSA方法计算了21种酚类模式底物与T. versicolor漆酶的结合自由能. 分子力学计算结果表明, 漆酶与底物的结合力主要来自Asp206和Asn264等残基与底物分子形成的分子间氢键, 并且Phe265残基和酚类底物的芳香环形成π-π相互作用. 量子化学计算表明, 芳环上取代基的推拉电子效应显著影响协同电子转移的底物去质子化过程, 其中推电子能力较强的—NH₂, —OH, —OCH₃和—CH＝CHCH₃等基团能够明显增强酚羟基反应活性, 而吸电子的—CONH₂和—Cl则具有相反的效应.

关键词: 漆酶, 结合力, 反应活性, 分子力学, 量子化学, 酚类底物

Abstract:

The binding affinity and reactivity between laccase and phenolic substrates were investigated with bioinformatics analysis, molecular dynamics simulation and quantum chemical calculation. Sequence and structure alignments indicate that the substrate-binding pocket of the laccases include certain conserved amino acid(AA) residues, such as Asp/Glu206, Asn/His208, Asn264, Gly392, His458(using the AA sequence number of PDB: 1KYA, a laccase from Trametes versicolor). Accordingly, the binding affinity between the laccase and the modeled 21 phenolic substrates were calculated with the MM-GBSA method. As a result of the molecular modeling, the inter-molecular hydrogen bonding between the hydroxyl group and Asp206/Asn264, and the π-π interaction between the phenyl group and Phe265, are essential for binding phenolic substrates to the laccase. The quantum chemistry calculations indicate that electronic effects of the additional substituent groups on the substrates would affect reductivity significantly, in particular for the collaborative deprotonation. The electron-donating groups, such as —NH₂, —OH, —OCH₃ and —CH=CHCH₃, enhance the substrate reactivity, while the electron-withdrawing groups not, e.g. —C(=O)NH₂ and —Cl. Our theoretical studies revealed that the binding affinity and reactivity stem from the different physiochemical nature, casting fundamental insights to future molecular design of laccase-mediator system.

Key words: Laccase, Affinity, Reactivity, Molecular modeling, Quantum chemistry, Phenolic substrate

中图分类号:

O641.3

TrendMD:

齐艳兵, 朱吉人, 孙尧金, 杜芸, 褚建君, 石婷, 赵一雷, 王晓雷. 漆酶与酚类模式底物的结合及反应活性的理论研究. 高等学校化学学报, 2014, 35(4): 776.

QI Yanbing, ZHU Jiren, SUN Yaojin, DU Yun, CHU Jianjun, SHI Ting, ZHAO Yilei, WANG Xiaolei. Theoretical Studies of the Binding-affinity and Reactivity Between Laccase and Phenolic Substrates^†. Chem. J. Chinese Universities, 2014, 35(4): 776.

图/表 8

参考文献 32

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Substrate	ΔE_b/(kJ·mol^-1)
Substrate	Leu164	Asp206	Asn208	Phe239	Asn264	Phe265	Pro391	Gly392	Ala393	Pro394	Hie458
1	-1.34	9.45	-1.34	-0.42	-3.51	-3.55	-0.29	-2.80	0	-2.76	-1.00
2	-2.42	-1.42	-0.59	-0.29	-1.67	-4.05	-0.38	-2.13	-0.79	-1.80	-1.76
3	-0.84	-8.99	-1.96	-0.67	-3.64	-3.30	-0.25	-0.84	-1.42	-1.21	-1.55
4	-1.09	-2.26	-0.96	-0.42	-2.55	-3.64	-0.29	-1.38	-0.67	-1.88	-1.05
5	-0.75	9.15	-2.80	-0.67	-5.27	-3.34	-0.25	-1.21	-1.00	-2.22	-0.79
6	-0.84	-4.39	-4.68	-0.96	-6.73	-4.39	-0.25	-0.96	-0.42	-2.72	-2.09
7	-2.63	2.30	-0.50	-0.33	-0.84	-4.05	-1.05	-2.34	-0.92	-2.22	-2.68
8	-1.46	6.44	-2.01	-0.50	-5.73	-4.56	-0.25	-3.39	-0.67	-3.97	-0.75
9	-2.13	9.78	-0.96	-0.50	-5.35	-3.01	-0.38	-3.55	-0.38	-2.51	-0.54
10	-1.71	8.40	-0.84	-0.46	-6.10	-3.51	-0.33	-3.55	-2.97	-2.93	-0.71
11	-1.34	6.77	-2.05	-0.46	-6.10	-4.35	-0.25	-2.88	-1.25	-4.22	-1.09
12	-2.63	7.15	-2.05	-0.54	-3.89	-3.68	-0.46	-4.39	-0.29	-2.88	-0.88
13	-2.26	9.24	-0.92	-0.42	-4.47	-3.14	-0.50	-4.47	0.04	-1.71	-0.71
14	-2.34	3.76	-1.09	-0.46	-1.25	-4.60	-0.42	-2.63	-0.42	-2.55	-1.30
15	-2.51	-6.94	-0.75	-0.42	-1.59	-3.55	-0.46	-2.88	-0.59	-1.80	-1.00
16	-1.30	8.74	-1.76	-0.46	-6.23	-4.01	-0.33	-2.84	-0.04	-3.05	-0.88
17	-1.50	8.28	-1.00	-0.46	-4.72	-4.85	-0.25	-2.30	-1.30	-3.55	-0.88
18	-2.30	10.24	-0.88	-0.46	-2.93	-6.60	-5.77	-5.64	-3.68	-3.59	-5.98
19	-8.53	8.40	-0.13	-0.21	0.04	-3.05	-4.81	-6.60	1.34	-1.67	-4.39
20	-4.97	8.07	-0.75	-0.38	-4.18	-5.31	-0.92	-4.93	-1.38	-5.94	-3.72
21	-2.68	9.91	-1.38	-0.42	-5.31	-7.77	-1.21	-3.68	-3.47	-3.64	-3.59
Average	-2.26	4.85	-1.38	-0.46	-3.93	-4.22	-0.92	-3.09	-0.96	-2.80	-1.76

Substrate	ΔE_b/(kJ·mol^-1)
Substrate	Leu164	Asp206	Asn208	Phe239	Asn264	Phe265	Pro391	Gly392	Ala393	Pro394	Hie458
1	-1.34	9.45	-1.34	-0.42	-3.51	-3.55	-0.29	-2.80	0	-2.76	-1.00
2	-2.42	-1.42	-0.59	-0.29	-1.67	-4.05	-0.38	-2.13	-0.79	-1.80	-1.76
3	-0.84	-8.99	-1.96	-0.67	-3.64	-3.30	-0.25	-0.84	-1.42	-1.21	-1.55
4	-1.09	-2.26	-0.96	-0.42	-2.55	-3.64	-0.29	-1.38	-0.67	-1.88	-1.05
5	-0.75	9.15	-2.80	-0.67	-5.27	-3.34	-0.25	-1.21	-1.00	-2.22	-0.79
6	-0.84	-4.39	-4.68	-0.96	-6.73	-4.39	-0.25	-0.96	-0.42	-2.72	-2.09
7	-2.63	2.30	-0.50	-0.33	-0.84	-4.05	-1.05	-2.34	-0.92	-2.22	-2.68
8	-1.46	6.44	-2.01	-0.50	-5.73	-4.56	-0.25	-3.39	-0.67	-3.97	-0.75
9	-2.13	9.78	-0.96	-0.50	-5.35	-3.01	-0.38	-3.55	-0.38	-2.51	-0.54
10	-1.71	8.40	-0.84	-0.46	-6.10	-3.51	-0.33	-3.55	-2.97	-2.93	-0.71
11	-1.34	6.77	-2.05	-0.46	-6.10	-4.35	-0.25	-2.88	-1.25	-4.22	-1.09
12	-2.63	7.15	-2.05	-0.54	-3.89	-3.68	-0.46	-4.39	-0.29	-2.88	-0.88
13	-2.26	9.24	-0.92	-0.42	-4.47	-3.14	-0.50	-4.47	0.04	-1.71	-0.71
14	-2.34	3.76	-1.09	-0.46	-1.25	-4.60	-0.42	-2.63	-0.42	-2.55	-1.30
15	-2.51	-6.94	-0.75	-0.42	-1.59	-3.55	-0.46	-2.88	-0.59	-1.80	-1.00
16	-1.30	8.74	-1.76	-0.46	-6.23	-4.01	-0.33	-2.84	-0.04	-3.05	-0.88
17	-1.50	8.28	-1.00	-0.46	-4.72	-4.85	-0.25	-2.30	-1.30	-3.55	-0.88
18	-2.30	10.24	-0.88	-0.46	-2.93	-6.60	-5.77	-5.64	-3.68	-3.59	-5.98
19	-8.53	8.40	-0.13	-0.21	0.04	-3.05	-4.81	-6.60	1.34	-1.67	-4.39
20	-4.97	8.07	-0.75	-0.38	-4.18	-5.31	-0.92	-4.93	-1.38	-5.94	-3.72
21	-2.68	9.91	-1.38	-0.42	-5.31	-7.77	-1.21	-3.68	-3.47	-3.64	-3.59
Average	-2.26	4.85	-1.38	-0.46	-3.93	-4.22	-0.92	-3.09	-0.96	-2.80	-1.76

Position	Model	R(2-ortho)	R(6-ortho)	R(para)	ΔΔG/(kJ·mol^-1)	ΔΔG'/(kJ·mol^-1)	Taft σ^*	σ_para
2-ortho-	4	NH₂	H	H	0.00		0.62
	3	OH	H	H	39.33		1.34
	5	OCH₃	H	H	40.84		1.81
	7	CH＝CHCH₃	H	H	43.72		0.36
	1	H	H	H	55.76		0.49
	2	Cl	H	H	78.50		2.96
	6	CONH₂	H	H	98.69		1.68
ortho,	9	OCH₃	H	NH₂	-8.78	-49.62^a		-0.66
para-	10	OCH₃	H	OH	19.31	-21.53^a		-0.37
	8	OCH₃	H	Cl	46.44	5.60^a		0.23
	11	OCH₃	H	CONH₂	53.88	13.04^a		0.36
2,6-	12	OCH₃	OCH₃	H	-19.77	-60.61^a	3.62
	13	OCH₃	OH	H	-0.84	-41.67^a	3.15
	15	OH	OH	H	45.48	6.14^b	2.68
	14	Cl	Cl	H	76.37	-2.17^c	5.92
Lignin	21	OCH₃	H	CHR''OH	11.75
model	18	OCH₃	PhR	CH₂OH	25.50
compounds	20	OCH₃	H	CHR'OH	37.91
	16	OCH₃	H	CH₂OH	42.85
	17	OCH₃	H	CHO	72.31
	19	OCH₃	H	COR'	76.95

Position	Model	R(2-ortho)	R(6-ortho)	R(para)	ΔΔG/(kJ·mol^-1)	ΔΔG'/(kJ·mol^-1)	Taft σ^*	σ_para
2-ortho-	4	NH₂	H	H	0.00		0.62
	3	OH	H	H	39.33		1.34
	5	OCH₃	H	H	40.84		1.81
	7	CH＝CHCH₃	H	H	43.72		0.36
	1	H	H	H	55.76		0.49
	2	Cl	H	H	78.50		2.96
	6	CONH₂	H	H	98.69		1.68
ortho,	9	OCH₃	H	NH₂	-8.78	-49.62^a		-0.66
para-	10	OCH₃	H	OH	19.31	-21.53^a		-0.37
	8	OCH₃	H	Cl	46.44	5.60^a		0.23
	11	OCH₃	H	CONH₂	53.88	13.04^a		0.36
2,6-	12	OCH₃	OCH₃	H	-19.77	-60.61^a	3.62
	13	OCH₃	OH	H	-0.84	-41.67^a	3.15
	15	OH	OH	H	45.48	6.14^b	2.68
	14	Cl	Cl	H	76.37	-2.17^c	5.92
Lignin	21	OCH₃	H	CHR''OH	11.75
model	18	OCH₃	PhR	CH₂OH	25.50
compounds	20	OCH₃	H	CHR'OH	37.91
	16	OCH₃	H	CH₂OH	42.85
	17	OCH₃	H	CHO	72.31
	19	OCH₃	H	COR'	76.95

漆酶与酚类模式底物的结合及反应活性的理论研究

Theoretical Studies of the Binding-affinity and Reactivity Between Laccase and Phenolic Substrates^†

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漆酶与酚类模式底物的结合及反应活性的理论研究

Theoretical Studies of the Binding-affinity and Reactivity Between Laccase and Phenolic Substrates†

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Theoretical Studies of the Binding-affinity and Reactivity Between Laccase and Phenolic Substrates^†