高等学校化学学报 ›› 2018, Vol. 39 ›› Issue (2): 255-262.doi: 10.7503/cjcu20170586

• 物理化学 • 上一篇    下一篇

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

李文娟, 赵一雷()   

  1. 上海交通大学生命科学技术学院, 微生物代谢国家重点实验室, 上海 200240
  • 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: yileizhao@sjtu.edu.cn
  • 基金资助:
    国家自然科学基金(批准号: 21377085)资助

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

LI Wenjuan, ZHAO Yilei*()   

  1. State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology,Shanghai Jiao Tong University, Shanghai 200240, China
  • Received:2017-08-31 Online:2018-02-10 Published:2017-12-20
  • Contact: ZHAO Yilei E-mail:yileizhao@sjtu.edu.cn
  • Supported by:
    † Supported by the National Natural Science Foundation of China(No.21377085)

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.

关键词: 漆酶, 耐盐性, 系统发生树, 随机加速分子动力学模拟, 蛋白质内部分子输运

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

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