Salt Tolerance of T. Versicolor Laccase: Bioinformatics Study and Internal Transportation of Chloride, Dioxygen, and Water†

doi:10.7503/cjcu20170586

Abstract

Abstract:

Laccase is a group of multicopper polyphenol oxidase that can catalyze oxidation of lignin and other molecules. Even though laccase is highly potential in energy and environment sciences, its applications are limited because of poor salt tolerance of commercial white rot fungi(T. versicolor) laccase. In this paper, bioinformatics analysis was conducted on available sequences and structures in protein data bank(PDB) database, and internal transportation of chloride, dioxygen, and water molecules were studied in more detail. Random acceleration molecular dynamics simulations, with a small randomly oriented force to exert small molecule from the laccase active site, indicated that five transportation channels(p1—p5) existed in T. versicolor laccase. Among them, p1, p3, and p4 were consistent with results of the previous literatures, while p2 and p5 were new transport pathways. In particular, internal chloride transportation was found to be more constrained than those for oxygen and water molecules, dominantly via p1 and p4 channels. Phylogenetic tree analysis indicated that, besides structural conservation for laccases, most salt-resistant laccase were expressed by bacteria, rather than plants and fungi. Moreover, it was found that acidic and aromatic amino acid residues were significantly enriched around the p4 channel in the high-tolerant species, which may help to prevent the chloride transportation and increase its saline-tolerance.

Key words: Laccase, Salt tolerance, Phylogenetic tree, Random acceleration molecular dynamics simulation, Protein internal molecules transportation

CLC Number:

O641

TrendMD:

LI Wenjuan, ZHAO Yilei. Salt Tolerance of T. Versicolor Laccase: Bioinformatics Study and Internal Transportation of Chloride, Dioxygen, and Water^†[J]. Chem. J. Chinese Universities, 2018, 39(2): 255.

Figures/Tables 7

Scheme 1 Graphical representation of laccase structure with 3D surface model(A) and 2D topological diagram(B) Representative structure based on PDB# 1KYA in protein data bank, and the four copper atoms in orange and the three domains in salmon, green and teal, respectively.

Fig.1 Active sites of single and tri-nuclear copper clustersX and Y were the positions of two oxygen atoms from dioxygen molecule, in which T3-Cu ligand X=OH-, O2 and Cl-, meanwhile T2-Cu ligand Y=OH-, H2O, and Cl-, respectively. The dashed lines denoted coordination to the copper cations.

Fig.2 Phylogenetic tree of 29 laccase sequences based on sequence and structure alignment(A) and 26 superposed laccase structures with the POSA program(B) (A) Halotolerant laccases in green color; (B) the insets emphasize the comparison between T. versicolor(gray, from ascomycotas), basidio(green), and bacterial laccases(blue).

Fig.3 Transportation channels towards T3-Cu(A) and T2-Cu(B), and pathways exhibited with ligand snapshots in the RAMD trajectories of X-Cl-(C), Y-Cl-(D), X-O2(E) and Y-H2O(F) Each trajectory was shown in one color in Fig.3(C—F).

Fig.4 Constructions of tunnels p1(A), p2(B), p3(C), p4(D) and p5(E)The color-coding is same as Fig.1. The important residues surrounding the tunnel are shown as sticks.

Fig.5 Sequence alignment of residues constructing p1 tunnel in laccase

Table 1 Partition of internal transportation calculated with the RAMD simulations

No.	Ligand	10²⁴ Accel./(kJ·mol^-1· nm^-1·g^-1)	r_min/nm	Number of successful egress	Pathway	Frequency
Ⅰ	X=Cl^-	15.12	0.0120	18	p1a	12/18
					p2	3/18
					p3	1/18
					p4	1/18
Ⅱ	Y=Cl^-	7.56	0.0050	18	p4	18/18
Ⅱ	X=O₂	5.29	0.0042	18	p1a	3/18
					p1b	3/18
					p1c	1/18
					p2	6/18
					p3	1/18
					Others	4/18
Ⅳ	Y=H₂O	5.29	0.0042	13	p4	11/13
					p5a	1/13
					p5b	1/13

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