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

doi:10.7503/cjcu20131287

Abstract

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

CLC Number:

O641.3

TrendMD:

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^†[J]. Chem. J. Chinese Universities, 2014, 35(4): 776.

Figures/Tables 8

References 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