高等学校化学学报 ›› 2018, Vol. 39 ›› Issue (2): 255.doi: 10.7503/cjcu20170586
收稿日期:
2017-08-31
出版日期:
2018-02-10
发布日期:
2017-12-20
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:基金资助:
Received:
2017-08-31
Online:
2018-02-10
Published:
2017-12-20
Contact:
ZHAO Yilei
E-mail:yileizhao@sjtu.edu.cn
Supported by:
摘要:
运用生物信息学方法分析了各物种漆酶的耐盐性差异, 并利用随机加速动力学模拟计算揭示了白腐菌漆酶内部连接三铜活性中心(TNC)的氯离子、 氧气和水分子的可能输运通路. 生物信息学系统发生树和结构比对分析表明, 担子真菌、 子囊真菌与细菌漆酶具有较高的结构保守性; 通过随机加速动力学模拟发现, 白腐菌T. versicolor漆酶内部有5条小分子输运通道(p1~p5), 其中p2和p5为新的输运通道; 与氧气和水分子输运不同, 氯离子在漆酶内部输运时受到明显约束, 以较高的几率通过p1和p4输运通道. 高耐盐漆酶的p1通道周边富集了更多酸性和芳香性氨基酸残基, 降低了氯离子的输运效率, 从而提高其耐盐性.
中图分类号:
TrendMD:
李文娟, 赵一雷. 白腐菌漆酶耐盐性的生物信息学研究及氯离子、 氧气和水分子输运通道分析. 高等学校化学学报, 2018, 39(2): 255.
LI Wenjuan, ZHAO Yilei. Salt Tolerance of T. Versicolor Laccase: Bioinformatics Study and Internal Transportation of Chloride, Dioxygen, and Water†. Chem. J. Chinese Universities, 2018, 39(2): 255.
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.
No. | Ligand | 1024 Accel./(kJ·mol-1· nm-1·g-1) | rmin/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 |
Table 1 Partition of internal transportation calculated with the RAMD simulations
No. | Ligand | 1024 Accel./(kJ·mol-1· nm-1·g-1) | rmin/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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