[1]王四华,黄可君,张光亚.以分子动力组学的方法探究嗜盐酶的嗜盐机理[J].华侨大学学报(自然科学版),2013,34(2):169-175.[doi:10.11830/ISSN.1000-5013.2013.02.0169]
 WANG Si-hua,HUANG Ke-jun,ZHANG Guang-ya.Halophilic Mechanism of the Halophilic Enzymes Based on the Molecule Dynameomics Method[J].Journal of Huaqiao University(Natural Science),2013,34(2):169-175.[doi:10.11830/ISSN.1000-5013.2013.02.0169]
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以分子动力组学的方法探究嗜盐酶的嗜盐机理()
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《华侨大学学报(自然科学版)》[ISSN:1000-5013/CN:35-1079/N]

卷:
第34卷
期数:
2013年第2期
页码:
169-175
栏目:
出版日期:
2013-03-20

文章信息/Info

Title:
Halophilic Mechanism of the Halophilic Enzymes Based on the Molecule Dynameomics Method
文章编号:
1000-5013(2013)02-0169-07
作者:
王四华 黄可君 张光亚
华侨大学 化工学院, 福建 厦门 361021
Author(s):
WANG Si-hua HUANG Ke-jun ZHANG Guang-ya
College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
关键词:
嗜盐酶 非嗜盐酶 动力组学 分子动力学模拟 嗜盐机理
Keywords:
halophilic enzyme non-halophilic enzyme dynameomics molecular dynamics simulation halophilic mechanism
分类号:
Q937;O648.121
DOI:
10.11830/ISSN.1000-5013.2013.02.0169
文献标志码:
A
摘要:
通过分子动力组学的方法,从原子尺度上分析4组嗜盐酶及其同源非嗜盐酶的分子动力学特性.结果发现:嗜盐酶所形成的盐桥和氢键明显多于非嗜盐酶,嗜盐酶的溶剂可及性表面要小于非嗜盐酶.通过比较嗜盐与非嗜盐的均方根偏差、回旋半径及末端距等参数,发现嗜盐酶的结构较非嗜盐酶更具刚性.同时,非嗜盐酶多个部位的氨基酸残基柔性比嗜盐酶的要大很多.研究表明:能形成较多的盐桥、氢键,较小的溶剂可及性表面和整体结构的刚性,很可能是嗜盐酶在高盐环境中维持其结构稳定的主要原因.
Abstract:
We analyzed the dynamics characteristics of the four groups halophilic enzyme and non-halophilic homologs by molecule dynameomics method in the atomistic scale. The results found that: halophilic enzyme can form more salt bridges and hydrogen bonds than non-halophilic enzyme, the solvent accessible surface areas of halophilic enzyme are larger than non-halophilic enzyme. We also found that the structure of halophilic enzyme is more rigid by comparing the root mean square deviation(RMSD), radius of gyration and end distance. Besides, the flexibility of the amino acids of non-halophilic enzyme is more large than halophilic enzyme. It can be supposed that the main factors that halophilic enzymes can maintain their structure stability in high saline conditions are rich in salt bridges and hydrogen bonds, smaller solvent accessible surface area and structure rigidity.

参考文献/References:

[1] KUSHNER D J.Life in high salt and solute concentrations[M].London:Academic Press,1978:317-368.
[2] KAMEKURA M.Diversity of extremely halophilic bacteria[J].Extremophiles,1998,2(3):289-295.
[3] DOMINIQUE M,CHRISTINE E,GIUSEPPE Z.Halophilic adaptation of enzymes[J].Extremophiles,2000,4(2):91-98.
[4] VENTOSA A J,NIETO J J,OREN A.Biology of moderatelyhalophilic aerobic bacteria[J].Microbiolol Biol Rev,1998,62(2):504-544.
[5] GALINSKI E A,TRUPER H G.Microbial behaviour in salt-stresed ecosystems[J].FEMS Microbiol Rev,1994,15(2/3):95-108.
[6] AHARON O.Microbial life at high salt concentrations: Phylogenetic and metabolic diversity[J].Saline Systems,2008,4(2):(doi:10.1186/1746-1448-4-2).
[7] DAVID A C B,AMANDA LJ,SCHAEFFER R D,et al.Dynameomics: Mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations[J].Protein Eng Des Sel,2008,21(6):353-368.
[8] 欧阳芳平,徐慧,郭爱敏,等.分子模拟方法及其在分子生物学中的应用[J].生物信息学,2005(1):33-36.
[9] ERIC D M,WILLIAM W P,VALERIE D.Temperature dependence of the flexibility of thermophilic and mesophilic flavoenz ymes of the niteoedu-ctase fold[J].Protein Eng Des Sel,2010,23(5):327-336.
[10] TATYANA B M,ANNA V G,MARIA G K,et al.Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and fold unfold method[J].J Bioinformatics and Computational Bio,2010,8(3):377-394.
[11] SANGEETA K,DEBJANI R.Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation[J].J Molecular Graphics and Modeling,2009,27(8):871-880.
[12] PIEPER U,KAPADIA G,MEVARECH M,et al.Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon[J].Structure,1998,16(1):75-88.
[13] FIORAVANTI E,VELLIEUX F M,AMARA P,et al.Specific radiation damage to acidic residues and its relation to their chemical and structural environment[J].J Synchrotron Rad,2007,14(1):84-91.
[14] ANDY W,PATRIK J,RONNALD V,et al.Structural and biochemical characterization of a halophilic archaeal alkaline phosphatase[J].J Mol Bio,2010,400(1/2):52-62.
[15] ALOJORO Y,TAKEFUMI I,MASAHIRO K,et al.Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphatekinases[J].Biophysical Journal,2009,96(11):4692-4700.
[16] BYSTROFF C,OATLEY S J,KRAUT J.Crystal structures of Escherichia coli dihydrofolate reductase: The NADP+ holoenzyme and the folate-NADP+ ternary complex: Substrate binding and a model for the transition state[J].Biochemistry,1990,29(13):3263-3277.
[17] ALEXANDRA B,BJORN D,DIMITRIOS M,et al.Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface[J].J Mol Biol,2004,341(5):1215-1226.
[18] WANG J,STIEGLITZ K A,KANTROWITZ E R.Metal specificity is correlated with two crucial active site residues in Escherichia coli alkaline phosph-atase[J].Biochemistry 2005,44(23):8378-8386.
[19] GAURI M,ANITA A,DIVYA D,et al. Crystal structure of the Bacillus anthracis nucleoside diphospate kinase and its characterization reveals an enzyme adapted to perform under stress conditions[J].Proteins,2009,76(2):496-506.
[20] PHILLIPS J C,BRAUN R,WANG W.Scalable molecular dynamic with NAMD[J].Comput Chem,2005,26(16):1781-1802.
[21] HUMPHREY W,DALKE A,SCHULTEN K.VMD: Visual molecular dynamics[J].J Mol Graphics,1996,14(1):33-38.
[22] MACKARREL J,AD ashford,BELLOT D,et al.All-atom empirical potential for molecular modeling and dynamics studies of proteins[J].J Phys Chem,1998,102(18):3586-3616.
[23] DARDEN T,YORK D,PEDERSEN L.Particle mesh ewald: An N~log(N)method for ewald sums in large systems[J].J Chem Phys,1993,98(12):10089-10092.
[24] COSTENARO L,ZACCAI G,EBEL C.Link between protein-solvent and weak protein-protein interactions gives insight into halophilic adaptation[J].Biochemistry,2002,41(44):13245-13252.
[25] TARDIEU A,BONNETÉ F,FINET S,et al.Understanding salt or PEG induced attractive interactions to crystallize biological macromolecules[J].Acta Crystallogr Sect D Biol Crystallogr,2002,58(10):1549-1553.
[26] TADEO X,LÓPEZ-MÉNDEZ B,TRIGUEROS T.Structural basis for the aminoacid composition of proteins from halophilic archea[J].PLoS Biol,2009,7(12):e1000257.
[27] BENACHENHOU N,BALDACCI G.The genes for a halophilic glutamate dehydrogenase, sequene transcription and phylogenetic implications[J].Mol Gen Genet,1991,230(3):345-352.
[28] BALDACCI G,GUINET F,TILLIT J,et al.Functional implications related to the gene structure of the elongation factor EF-Tu from Halobacterium marismortui[J].Nucl Acids Res,1990,18(3):507-511.
[29] MEVARECH M F,FROLOW L M.Halophilic enzymes: Proteins with a grain of salt[J].Biophys Chem,2000,86(2/3):155-164.
[30] EISENBERG H.Life in unusual environments: Progress in understanding the structure and function of enzymes from extreme halophilic bacteria[J].Arch Biochem Biophys,1995,318(1):1-5.
[31] COQUELLE N,TALON R,JUERS D H.Gradual adaptive changes of a protein facing high salt concentrations[J].J Mol Biol,2010,404(3):493-505.
[32] FROLOW F,HAREL M,SUSSMAN J L.Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin[J].Nat Struct Biol,1996,3(5):452-458.
[33] ZACCAI G,CENDRIN F,HAIK Y,et al.Stabilization of halophilic malate dehydrogenase[J].J Mol Biol,1989,208(3):491-500.
[34] EBEL C,COSTENARO L,PASCU M,et al.Solvent interactions of halophilic malate dehydrogenase[J].Biochemistry,2002,41(44):13234-13244.
[35] 刘铁汉,周培瑾.极端嗜盐硫解酶基因的克隆和氨基酸组成分析[J].微生物学报,2002,42(4):406-410.
[36] SELIM C,BERNA S A,AZIZ A D,et al.Proteomic insight into phenolic adaptation of a moderately halophilic Halomona sp. strain AAD12[J].Can J Microbiol,2011,57(4):295-302.
[37] LIANG Chen-hui,YI Wei,LI Bin.Case study of hypersaline organic wastewater treatment with SBBR process[J].Pollution Control Technology,1998,14(4):226-228.
[38] BIRGE R R.Photophysics and molecular electronic applications of the rhodopsins[J].Annu Rev Phys Chem,1990,41:683-733.
[39] SHI Hai-ping,SU Tao.Study on mcrobiol frmentation of cllecting for ply-β-hydroxybutyrate[J].Food and Fermentation Industries,1998,24(2):79-82.
[40] EICHLER J.Biotechnological uses of archaeal extremozymes[J].Biotechnology Advances,2001,19(4):261-278.
[41] WANG Shi-fen,YANG Jian.Treatment of petro-fermentation wastewater with high salt content[J].Water and Wastewater Engineering,1999,25(3):35-38.

备注/Memo

备注/Memo:
收稿日期: 2012-03-11
通信作者: 张光亚(1975-),男,教授,主要从事酶与生物信息学的研究.E-mail:zhgyghh@hqu.edu.cn.
基金项目: 国家自然科学基金资助项目(20806031); 福建省自然科学基金资助项目(2007J0360); 福建省高校新世纪优秀人才支持计划项目(07176C02); 华侨大学基本科研业务费专项基金资助项目(JB-GJ1006)
更新日期/Last Update: 2013-03-20