Please wait a minute...

中国生物工程杂志

CHINA BIOTECHNOLOGY
中国生物工程杂志
中国生物工程杂志  2015, Vol. 35 Issue (7): 68-75    DOI: 10.13523/j.cb.20150710
技术与方法     
脱氮硫杆菌硫化合物载体SoxYZ蛋白的同源建模和结构分析
张晨晨, 孟志忠, 陆远芳, 陈新, 李杉
华南理工大学生物科学与工程学院 广州 510006
Homology Modeling and Structure Analysis of SoxYZ: A Carrier of Sulfur Compounds from Thiobacillus denitrificans
ZHANG Chen-chen, MENG Zhi-zhong, LU Yuan-fang, CHEN Xin, LI Shan
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
 全文: PDF(1609 KB)   HTML
摘要：

脱氮硫杆菌(Thiobacillus denitrificans)中的Sox蛋白在硫代谢过程中起着至关重要的作用,硫化合物需先与硫氧化基因族(sox)编码的蛋白质SoxYZ二聚体共价连接后才能与其他酶发生相互作用。利用同源建模法构建硫化合物载体 SoxYZ蛋白的二聚体结构并验证了其合理性。二聚体相互作用分析发现SoxYZ蛋白的溶剂可及表面积(solvent accessible surface,SAS)为10 922.9 Å2, 疏水率为50.85%;亚基SoxY和SoxZ界面处共含有12个氢键和1个Π键来维持其三维结构的稳定性;二聚体表面呈现明显的正负电势互补,两亚基界面处氨基酸残基的VDW作用能和静电作用能分别为－80.925 13kcal/mol和－323.856 57kcal/mol,这说明静电作用是二聚体形成的主要驱动力;SoxZ亚基的残基Thr28、Arg31、Lys32、Ser64、Gly65、Val66、Ser67对SoxY亚基活性位点构象的稳定有重要作用。
关键词： 脱氮硫杆菌;  二聚体;  同源建模;  蛋白质相互作用    
Abstract:

Sox system of Thiobacillus denitrificans plays a vital role in the metabolism of sulfur compounds, SoxYZ coding by the sulfur oxidizing gene cluster (sox) is known to be a sulfur covalently binding protein, which binds sulfur compounds to the other enzymes. The structure of SoxYZ heterodimer, the carrier of sulfur compounds, is constructed by using homology modeling and is proved to be reliable. Analysis of protein interactions find that the Solvent Accessible Surface(SAS) of SoxYZ is 10 922.9Å2, hydrophobicity is 50.85%; the interface between subunits SoxY and SoxZ contains a total of 12 hydrogen bonds and a pi bond which maintain the stability of the three-dimensional structure; the electrostatic potential of SoxYZ surface is obviously complementary, the VDW interaction energy and electrostatic interaction energy of residues at the interface is －80.925 13kcal/mol and －323.856 57kcal/mol, respectively which showed that the electrostatic interaction energy was the main driving force to form the heterodimer and the residues Thr28, Arg31, Lys32, Ser64, Gly65, Val66, Ser67 of SoxZ played an important role in the stability of active site of SoxY.
Key words: Thiobacillus denitrificans    Heterodimer    Homology modeling    Protein interaction
收稿日期: 2015-01-15 出版日期: 2015-07-25
ZTFLH:  Q71  
通讯作者: 李杉     E-mail: lishan@scut.edu.cn
服务　　
把本文推荐给朋友
加入引用管理器
E-mail Alert
RSS
作者相关文章　　

引用本文:

张晨晨, 孟志忠, 陆远芳, 陈新, 李杉. 脱氮硫杆菌硫化合物载体SoxYZ蛋白的同源建模和结构分析[J]. 中国生物工程杂志, 2015, 35(7): 68-75.

ZHANG Chen-chen, MENG Zhi-zhong, LU Yuan-fang, CHEN Xin, LI Shan. Homology Modeling and Structure Analysis of SoxYZ: A Carrier of Sulfur Compounds from Thiobacillus denitrificans. China Biotechnology, 2015, 35(7): 68-75.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20150710    或    https://manu60.magtech.com.cn/biotech/CN/Y2015/V35/I7/68


[1] 贡俊,张肇铭.脱氮硫杆菌氧化硫化氢过程中的生物氧化和化学氧化.环境科学学报,2006,26(3):477-482. Gong J, Zhang Z M. Biological and chemical oxidation during oxidation of hydrogen sulfide by Thiobacillus denitrificans. Acta Scientiae Circumstantiae, 2006,26(3):477-482.

[2] 李绪.脱氮硫杆菌在工业废气和废水脱硫脱氮中的应用研究.天津:天津大学,化工学院,2008. Li X. Study on treatment of Thiobacillus denitrificans in flue gas and waste water denitrification and desulfurization processes. Tianjin: Tianjin University, School of Chemical Engineering and Technology,2008.

[3] Friedrich C G, Bardischewsky F, Rother D, et al. Prokaryotic sulfur oxidation. Current Opinion in Microbiology, 2005,8(3): 253-259.

[4] 郑彦彬,王威.生物脱硫技术在煤化工领域应用的可能性.煤化工,2006,34(2):54-56. Zheng Y B, Wang W. Possible applications of biological desuiphurization technology in coal chemical Industry. Coal Chemical Industry, 2006,34(2):54-56.

[5] 张忠智,鲁莽,魏小芳,等.脱氮硫杆菌的生态特性及其应用.化学与生物工程,2005, 22(2):52-54. Zhang Z Z, Lu M, Wei X F, et al. Ecological characters and application of Thiobacillus denitrificans. Chemistry & Bioengineering, 2005,22(2):52-54.

[6] Sauvé V, Bruno S, Berks B C, et al. The SoxYZ complex carries sulfur cycle intermediates on a peptide swinging arm. The Journal of Biological Chemistry, 2007,282(32):23194-23204.

[7] Mohapatra B R, Gould W D, Dinardo O, et al. An overview of the biochemical and molecular aspects of microbial oxidation of inorganic sulfur compounds. CLEAN-Soil Air Water, 2008, 36(10-11): 823-829.

[8] 张志刚.耐热β-半乳糖苷酶的结构分析及同源建模.现代食品科技,2013,29(4):706-709. Zhang Z G. Structure analysis and homology modeling of thermostable β-galactosidase. Modern Food Science and Technology, 2013,29(4):706-709.

[9] 李军.纤维素酶E4的同源建模和分子对接研究.广州:华南理工大学,生物科学与工程学院,2012. Li J. Study on Homology Modeling and Molecular-docking Simulation of Cellulase E4. Guangzhou: South China University of Technology, School of Bioscience & Bioengineering, 2012.

[10] Beller H R, Chain PS G, Letain T E, et al. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. Journal of Bacteriology, 2006,188(4): 1473-1488.

[11] 徐钰.几类重要蛋白质的分子动力学模拟研究.长春:吉林大学,化学学院,2012. Xu Y. Theoretical Studies on the Catalytic Mechanisms of Several Important Enzymes. Changchun: Jilin University, College of Chemistry,2012.

[12] Bagchi A, Ghosh T C. A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon. Biochemical and Biophysical Research Communications, 2005,335(2):609-615.

[13] Ray S, Bagchi A. Structural analysis of the mode of interactions of SoxB protein with SoxYZ complex from Allochromatium vinosum in the global sulfur oxidation cycle. Computational Molecular Biology, 2013,3(1):1-5.

[14] 李书祥.柑橘绿霉菌CYP51的同源模建与分子对接模拟研究.武汉:华中师范大学,生命科学学院,2012. Li S X. Homology Modeling and Molecular Docking Studies of CYP51 from Penicillium digitatum. Wuhan: Central China Normal University, School of Life Sciences,2012.

[15] Laskowski R A, MacArthur M W, Moss D S, et al. PROCHECK-a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography,1993,26(2):283-291.

[16] 李霞.克雷伯杆菌中FNR蛋白三级结构模建及二聚作用研究.青岛:青岛科技大学,化工学院,2012. Li X. Tertiary Structure Modelling and Dimerization Study of the FNR Protein from Klebsiella pneumoniae. Qingdao: Qingdao University of Science & Technology, College of Chemical Engineering,2012.

[17] 陈正隆,徐为人,汤立达.分子模拟的理论与实践.北京:化学工业出版社,2007. Chen Z L, Xu W R, Tang L D. Theory and Practice of Molecular Modeling. Beijing: Chemical Industry Press,2007.

[18] 马晓慧.蛋白质二聚体相互作用和识别的计算机模拟.北京:北京工业大学,生命科学与生物工程学院,2012. Ma X H. Computer Simulation of the Interaction and Recognition of Protein Dimmers. Beijing: Beijing University of Technology, School of Life Sciences & Bioengineering,2012.
[1] 庞倩,陈晶,王小红,王佳. 基于噬菌体展示技术抗黄曲霉毒素B1单链抗体的筛选及其蛋白结构分析 *[J]. 中国生物工程杂志, 2018, 38(12): 41-48.
[2] 孟坤, 何庆瑜, 王通, 卢少华. 基于C6流式细胞仪平台应用FRET技术在活细胞中研究蛋白质相互作用[J]. 中国生物工程杂志, 2017, 37(5): 45-51.
[3] 黄欣媛, 范红波, 邹礼平. 蛋白片段互补分析技术研究进展[J]. 中国生物工程杂志, 2013, 33(11): 99-105.
[4] 陈思群, 孙自才, 陈建军, 陈晓晖. 糖-蛋白质相互作用在酶固定及蛋白质识别与分离中的应用[J]. 中国生物工程杂志, 2012, 32(04): 83-88.
[5] 吴丽, 杨成红, 邓思思, 周宇波, 钱旻, 臧奕. 应用酵母双杂交系统筛选AMPK相互作用蛋白[J]. 中国生物工程杂志, 2012, 32(02): 1-7.
[6] 黎玉叶, 李星星, 孙双双, 邹正渝, 张昀源, 段亮, 叶立伟, 武睿, 杨霞, 何通川, 周兰. S100A6蛋白对细胞中β-catenin水平的影响及可能机制[J]. 中国生物工程杂志, 2011, 31(11): 18-23.
[7] 胡凤娟, 王旭曼, 刘大岭, 姚冬生. 具蛋白酶抗性的Armillariella tabescens β-甘露聚糖酶MAN47的分子定向改造[J]. 中国生物工程杂志, 2011, 31(10): 75-82.
[8] 刘子杰,翁亚光,李素彦,施琼,蔡燕,刘斌,张燕,阎琛. 用FRET方法研究与Mps1蛋白有相互作用的CENP-E蛋白结构域[J]. 中国生物工程杂志, 2009, 29(04): 28-34.
[9] 范春香,崔韬,谷利,张韬,刘琦,赵焕英,赵春礼,杨慧. 帕金森病相关蛋白PINK1和α-突触核蛋白相互作用研究[J]. 中国生物工程杂志, 2008, 28(12): 7-11.
[10] 潘秋辉,杨松海,董群伟,孙奋勇. BMP2/7异源二聚体调控CIZ的表达与自身活性的关系[J]. 中国生物工程杂志, 2007, 27(9): 14-18.
[11] 李斌元, 何淑雅, 王桂良, 马云, 肖卫纯, 李洁, 孙春丽, 闵凌峰, 虞佳, NanbertZhong. Bax Inhibitor-1与Herp的相互作用[J]. 中国生物工程杂志, 2005, 25(11): 21-25.
[12] 张春莉, 李景利, 杜柏榕, 李秋生, 有红霞, 李金凤, 朱迅. 重组人红细胞生成素二聚体不同真核表达载体的构建及表达[J]. 中国生物工程杂志, 2005, 25(02): 39-44.
[13] 马海蓉, 李维琪. 酵母双杂交衍生系统[J]. 中国生物工程杂志, 2003, 23(2): 37-41.
[14] 李伯良, 李林, 吴家睿. 功能蛋白质组学[J]. 中国生物工程杂志, 1999, 19(4): 15-16.
[15] 李莉云, 刘国振, 刘丽娟. 担子菌交配型基因的克隆及功能研究进展[J]. 中国生物工程杂志, 1999, 19(1): 19-23.
主管：中国科学院 　主办：中国科学院文献情报中心 　中国生物技术发展中心 　中国生物工程学会