重组嗜热闪烁杆菌脂肪酶系的性质表征及嗜热磷酸三酯酶晶体结构解析
摘要
来源于嗜热微生物的嗜热酶具有独特的生物稳定性和催化活性,对嗜热酶结构-功能关系的研究已得到越来越多科学工作者的关注,该领域研究不仅将加深酶学和酶工程理论的发展,也为酶的工业应用奠定了基础。
论文第一部分克隆、表达、纯化和表征了来源于嗜热菌Fervidobacterium nodosum Rt17-B1的嗜热脂肪酶(FnL)和嗜热酯酶(FNE)。(1)FnL的序列同源性分析表明它与已知存在的脂肪酶基因的同源性低于30%,系统发育学分析表明它属于脂肪酶家族I,但与脂解酶家族I中现有的7个亚家族亲缘关系较远,因而将此嗜热脂肪酶所在的分支确定为脂肪酶家族I中的一个新的亚家族,并命名为family I.8;该重组脂肪酶的最适反应温度为70℃,最适pH为9.0,并且具有较高的热稳定性,其在60°C保温50小时几乎没有活力损失。底物选择性分析表明FnL偏好于水解中长链酰基(C_8-C_(12))的p-nitrophenyl酯底物,最适底物为p-nitrophenyl caprate,另外,FnL还能够水解链长在C_4到C_(16)范围的三甘油酯底物,最适底物为三丁酸甘油酯(C_4)。结构建模和分子模拟研究揭示了FnL发挥催化作用的结构基础及其底物选择性的分子机制。(2)FNE的序列同源性分析表明其与已知存在的GDSL酯酶基因的同源性低于30%,在其序列中发现了SGNH亚家族蛋白的4个保守模块,即Block I,Block II,Block III和Block V,推测其可能的催化三联体为Ser~8, Asp~(215)和His~(218),氧洞基团为Ser~8, Gly~(33)和Asn~(66)。该酯酶是GDSL家族中第一个来自嗜热微生物的酯酶。重组酶的最适反应温度为75℃,最适pH为8.5,FNE偏好于短链酰基(≤C_4)酯底物,最适底物为p-nitrophenyl acetate,它无法催化链长大于8的p-nitrophenyl酯底物的水解。通过与已知结构的酯酶进行结构比对,研究发现FNE位于活性位点之上存在一段插入序列,可能阻止了像三甘油酯等较大的底物分子与酶活性部位的接近,使FNE只能催化短链底物的水解。
论文第二部分运用蛋白质晶体学的技术对重组FnL、FNE以及嗜热菌Geobacillus kaustophilus HTA426的磷酸三酯酶GK1506进行结晶和结构解析。成功地获得了磷酸三酯酶GK1506的结晶,使用分子置换法解析了分辨率达2.6 A的晶体结构。结构分析表明: GK1506蛋白的三维结构为TIM滚筒状结构,活性位点由β折叠的C末端以及连接这些折叠和螺旋之间的loop构成,同时活性部位结合有两个Co~(2+);另外GK1506蛋白结构具有与其他OPH蛋白相似的三个结合口袋,分别是大的结合口袋,小的结合口袋和离去集团结合口袋。另外我们还通过定点突变确定了参与催化作用的重要氨基酸残基为His23,His25,His178,His206,Lys145和Asp266。GK1506与有机磷底物的对接实验结果表明,在该酶活性中心上方存在一个由柔性较高的loop形成的盖子结构,推测该段loop所具有的“开-关”功能的结构变化可能与酶分子的底物进出和对有机磷底物或内酯类底物的选择性机制有关。以上关于嗜热磷酸三酯酶晶体结构的研究为揭示结构与功能关系以及为蛋白质合理设计方面的研究奠定了理论基础。
The researches on thermophilic microorganisms and enzymes which have great impact on theoretical study and industrial applications have always been hot objects since 1990s’. This paper focuses on the characterization of the lipolytic hydrolyses from the thermophilic Fervidobacterium nodosum Rt17-B1 and the crystal structure of the phosphotriesterase from Geobacillus kaustophilus HTA426.
In the first part of my thesis, a gene coding for a putative lipase composed of 302 amino acids from Fervidobacterium nodosum Rt17-B1 was cloned and characterized. Phylogenetic analysis suggests that this novel lipase represents a new subfamily of family I of bacterial lipases, annotated as family I.8. The recombinant protein can catalyze the hydrolysis of p-nitrophenyl esters and shows substrate preference for p-nitrophenyl caprate with a k_(cat)/K_m of 22500 s~(-1)μM~(-1). Most importantly, it can hydrolyze triacylglycerols with long acyl chains. In the test conditions applied here it has a maximum activity at 70°C and pH 9.0 and displays extreme thermal stability. Interestingly, it was not only stable, but was also activated by treatment with polar organic solvents including propanol, acetone, dimethyl sulfoxide (DMSO) and N, N-dimethylformamide (DMF). Structural modeling showed that it is composed of anα/β-hydrolase fold and a lid domain comprised of fourα-helices. A canonical catalytic triad consisting of Ser119, Asp206 and His282 was verified by site-directed mutagenesis. Moreover based on the constructed model, the substrate specificity was explained by analyses in the aspects of the binding free energy, spatial obstruction, and interactions between enzyme and substrate in the active site. Moreover, a putative bacterial esterase encoded by Fond_1301 with typical GDSL family motifs from Fervidobacterium nodosum Rt17-B1 was cloned and characterized. Recombinant FNE exhibited the highest esterase activity (14,000 U/mg) with p-nitrophenyl acetate (pNPC_2) as substrate. The catalytic efficiency (k_(cat)/K_m) toward p-nitrophenyl acetate (C2_) was approximately 120-fold higher than toward p-nitrophenyl butyrate (C_4). No significant esterase activity was observed for the substrates with a chain length≥C_8. The monomeric enzyme has a molecular mass of 27.5 kDa and optimal activity around 75℃and at pH 8.5. Its thermostability is relatively high with a half-life of 80 min at 70℃, but less stable compared to some other hyperthermophilic esterases. A structural model was constructed with the acetylesterase from Aspergillus aculeatus as a template. The model covered most of the FNE. The structure showed anα/β-hydrolase fold and indicated the presence of a typical catalytic triad consisting of a serine, aspartate and histidine, which was verified by site-directed mutagenesis. Sequence analysis showed that FNE is only distantly related to other esterases. A comparison of the conserved motifs shared with GDSL proteins revealed that FNE should be grouped into GDSL family and was further classified as SGNH hydrolase.
In the second part of my thesis, the recombinant thermophilic phosphotriesterase GK1506 from Geobacillus kaustophilus HTA426 has been crystallized and the crystal structure of GK1506 has been determined by Singlewavelenth Anamolous Dispersion and molecular replacement.to 2.5 ?. The tertiary structure of this enzyme was anα/βbarrel in which the active site is located at the C-terminal ends of theβ-strands and in the loop regions connecting these strands to their subsequent helices. The active site of GK1506 contains the three substrate binding pockets found in other OPH enzymes: the small, large and leaving group pockets. The two metal ions was concluded in the active site of GK1506. site-directed mutagenesis lead us to make sure that His~(23), His~(25), His~(178), His~(206), Lys~(145) and Asp~(266) are important residues for catalytic function and substrate binding. The structure determination will illuminate the structure base of catalytic mechanisum. Moreover this knowledge can lead to the development of new and more efficient protein engineering strategies and a wide range of biotechnological applications.
论文第一部分克隆、表达、纯化和表征了来源于嗜热菌Fervidobacterium nodosum Rt17-B1的嗜热脂肪酶(FnL)和嗜热酯酶(FNE)。(1)FnL的序列同源性分析表明它与已知存在的脂肪酶基因的同源性低于30%,系统发育学分析表明它属于脂肪酶家族I,但与脂解酶家族I中现有的7个亚家族亲缘关系较远,因而将此嗜热脂肪酶所在的分支确定为脂肪酶家族I中的一个新的亚家族,并命名为family I.8;该重组脂肪酶的最适反应温度为70℃,最适pH为9.0,并且具有较高的热稳定性,其在60°C保温50小时几乎没有活力损失。底物选择性分析表明FnL偏好于水解中长链酰基(C_8-C_(12))的p-nitrophenyl酯底物,最适底物为p-nitrophenyl caprate,另外,FnL还能够水解链长在C_4到C_(16)范围的三甘油酯底物,最适底物为三丁酸甘油酯(C_4)。结构建模和分子模拟研究揭示了FnL发挥催化作用的结构基础及其底物选择性的分子机制。(2)FNE的序列同源性分析表明其与已知存在的GDSL酯酶基因的同源性低于30%,在其序列中发现了SGNH亚家族蛋白的4个保守模块,即Block I,Block II,Block III和Block V,推测其可能的催化三联体为Ser~8, Asp~(215)和His~(218),氧洞基团为Ser~8, Gly~(33)和Asn~(66)。该酯酶是GDSL家族中第一个来自嗜热微生物的酯酶。重组酶的最适反应温度为75℃,最适pH为8.5,FNE偏好于短链酰基(≤C_4)酯底物,最适底物为p-nitrophenyl acetate,它无法催化链长大于8的p-nitrophenyl酯底物的水解。通过与已知结构的酯酶进行结构比对,研究发现FNE位于活性位点之上存在一段插入序列,可能阻止了像三甘油酯等较大的底物分子与酶活性部位的接近,使FNE只能催化短链底物的水解。
论文第二部分运用蛋白质晶体学的技术对重组FnL、FNE以及嗜热菌Geobacillus kaustophilus HTA426的磷酸三酯酶GK1506进行结晶和结构解析。成功地获得了磷酸三酯酶GK1506的结晶,使用分子置换法解析了分辨率达2.6 A的晶体结构。结构分析表明: GK1506蛋白的三维结构为TIM滚筒状结构,活性位点由β折叠的C末端以及连接这些折叠和螺旋之间的loop构成,同时活性部位结合有两个Co~(2+);另外GK1506蛋白结构具有与其他OPH蛋白相似的三个结合口袋,分别是大的结合口袋,小的结合口袋和离去集团结合口袋。另外我们还通过定点突变确定了参与催化作用的重要氨基酸残基为His23,His25,His178,His206,Lys145和Asp266。GK1506与有机磷底物的对接实验结果表明,在该酶活性中心上方存在一个由柔性较高的loop形成的盖子结构,推测该段loop所具有的“开-关”功能的结构变化可能与酶分子的底物进出和对有机磷底物或内酯类底物的选择性机制有关。以上关于嗜热磷酸三酯酶晶体结构的研究为揭示结构与功能关系以及为蛋白质合理设计方面的研究奠定了理论基础。
The researches on thermophilic microorganisms and enzymes which have great impact on theoretical study and industrial applications have always been hot objects since 1990s’. This paper focuses on the characterization of the lipolytic hydrolyses from the thermophilic Fervidobacterium nodosum Rt17-B1 and the crystal structure of the phosphotriesterase from Geobacillus kaustophilus HTA426.
In the first part of my thesis, a gene coding for a putative lipase composed of 302 amino acids from Fervidobacterium nodosum Rt17-B1 was cloned and characterized. Phylogenetic analysis suggests that this novel lipase represents a new subfamily of family I of bacterial lipases, annotated as family I.8. The recombinant protein can catalyze the hydrolysis of p-nitrophenyl esters and shows substrate preference for p-nitrophenyl caprate with a k_(cat)/K_m of 22500 s~(-1)μM~(-1). Most importantly, it can hydrolyze triacylglycerols with long acyl chains. In the test conditions applied here it has a maximum activity at 70°C and pH 9.0 and displays extreme thermal stability. Interestingly, it was not only stable, but was also activated by treatment with polar organic solvents including propanol, acetone, dimethyl sulfoxide (DMSO) and N, N-dimethylformamide (DMF). Structural modeling showed that it is composed of anα/β-hydrolase fold and a lid domain comprised of fourα-helices. A canonical catalytic triad consisting of Ser119, Asp206 and His282 was verified by site-directed mutagenesis. Moreover based on the constructed model, the substrate specificity was explained by analyses in the aspects of the binding free energy, spatial obstruction, and interactions between enzyme and substrate in the active site. Moreover, a putative bacterial esterase encoded by Fond_1301 with typical GDSL family motifs from Fervidobacterium nodosum Rt17-B1 was cloned and characterized. Recombinant FNE exhibited the highest esterase activity (14,000 U/mg) with p-nitrophenyl acetate (pNPC_2) as substrate. The catalytic efficiency (k_(cat)/K_m) toward p-nitrophenyl acetate (C2_) was approximately 120-fold higher than toward p-nitrophenyl butyrate (C_4). No significant esterase activity was observed for the substrates with a chain length≥C_8. The monomeric enzyme has a molecular mass of 27.5 kDa and optimal activity around 75℃and at pH 8.5. Its thermostability is relatively high with a half-life of 80 min at 70℃, but less stable compared to some other hyperthermophilic esterases. A structural model was constructed with the acetylesterase from Aspergillus aculeatus as a template. The model covered most of the FNE. The structure showed anα/β-hydrolase fold and indicated the presence of a typical catalytic triad consisting of a serine, aspartate and histidine, which was verified by site-directed mutagenesis. Sequence analysis showed that FNE is only distantly related to other esterases. A comparison of the conserved motifs shared with GDSL proteins revealed that FNE should be grouped into GDSL family and was further classified as SGNH hydrolase.
In the second part of my thesis, the recombinant thermophilic phosphotriesterase GK1506 from Geobacillus kaustophilus HTA426 has been crystallized and the crystal structure of GK1506 has been determined by Singlewavelenth Anamolous Dispersion and molecular replacement.to 2.5 ?. The tertiary structure of this enzyme was anα/βbarrel in which the active site is located at the C-terminal ends of theβ-strands and in the loop regions connecting these strands to their subsequent helices. The active site of GK1506 contains the three substrate binding pockets found in other OPH enzymes: the small, large and leaving group pockets. The two metal ions was concluded in the active site of GK1506. site-directed mutagenesis lead us to make sure that His~(23), His~(25), His~(178), His~(206), Lys~(145) and Asp~(266) are important residues for catalytic function and substrate binding. The structure determination will illuminate the structure base of catalytic mechanisum. Moreover this knowledge can lead to the development of new and more efficient protein engineering strategies and a wide range of biotechnological applications.
引文
[1] Setter KO, Huber G., Segerer A. Hyperthermophilic microorganisms. FEMS. Microbiol Rev. 1990, 75: 117-124.
[2] Rothschild LJ, Mancinelli RL. Life in extreme environ- ments. Nature. 2001, 409: 1092-1101.
[3] Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and EucaryaProc. Nati. Acad. Sci. USA. 1990, 87: 4576-4579.
[4] James RB, Andrei NL. What makes a thermophile. Trends in Microbiology. 1998, 6: 349-351.
[5] Palackal N, Brennan Y, Callen WN, Dupree P, Frey G, Goubet F, Hazlewood GP, Healey S, Kang YE, Kretz KA, et al: An evolutionary route to xylanase process fitness. Protein. Sci. 2004, 13: 494-503.
[6] Cowan DA: Thermophilic proteins: stability and function in aqueous and organic solvents. Comp. Biochem. Physiol. A. Physiol. 1997, 118: 429-438.
[7] Polizzi KM, Bommarius AS, Broering JM, Chaparro-Riggers JF. Stability of bilcatalysts. Curr. Opin. Chem. Biol. 2007, 11: 220-225.
[8] Demirjian DC, Morís-Varas F, Cassidy CS. Enzymes from extremophiles. Curr. Opin. Chem. Biol. 2001, 5: 144-151.
[9] Becker P. Determination of the kinetic parameters during continuous cultivation of the lipase producing thermophile Bacillus sp. IHI-91 on olive oil. Appl. Microb. Biotechnol. 1997, 48: 184–190.
[10] Mozhaev V. Mechanism-based strategies for protein thermostabilization. Trends. Biotechnol. 1993, 11: 88–95.
[11] Krahe M, Antranikian G, Markel H. Fermentation of extremophilic microorganisms. FEMS. Microbiol. Rev. 1996, 18: 271–285.
[12] Kumar S, Nussinov R. How do thermophilic proteins deal with heat? A review. Cell. Mol. Life Sci. 2001, 58: 1216–1233.
[13]林影,卢嶸德。极端酶及其工业应用。工业微生物。2000, 30(2): 51-53。
[14] Haki GD, Rakshit SK. Developments in industrially important thermostable enzymes: a review. Bioresour. Technol. 2003, 89(1): 17-34.
[15] Batto M, Mathrani IM, Ahringb, et al. Appl. micobiol. Biotech. 1994, 41: 130-133.
[16] Bartolucci S, Rella R, Guagliardi A, Raia CA, Gambacorta A, Rosa MD, Rossi M. Malic enzyme from archaebacterium Sulfolobus solfataricus: purification, structure, and kinetic properties. J. Biol. Chem. 1987, 262: 7725-7731.
[17] Klug MJ, Markovetz AJ. Thermophilic bacterium isolated on n-tetradecane. Nature. 1967, 215: 1082-1083.
[18] Kargi F, Robinson JM. Removal of sulfur compounds from coal by the thermophilic organism sulfolobus acidocaldarius. Appl. Environ. Microbiol. 1982, 44: 878-883.
[19] McCutchen CM, Duffaud GD, Leduc P, Petersen AR, Tayal A, Khan SA, Kelly RM.. Characterization of extremely thermostable enzymatic breakers (alpha-1,6-galactosidase and beta-1,4-mannanase) from the hyperthemophilic bacterium Thermotoga neapolitana 5068 for hydrolysis of guar gum. Biltechnol. Bioent. 1996, 52: 332-339.
[20] IUPAC-IUB commission on nomenlature, enzyme nomenclature, academic press, New York. 1979, P6.
[21] Undurraga D, Markovits A, Erazo S. Cocoa butter equivalent through enzymic interesterification of palmoil midfraction. Process. Biochem. 2001, 36: 933-939.
[22] Zhang LQ, Zhang YD, Xu L, et al. Lipase catalyzed synthesis of RGD diamide in aqueous water-miscible organic solvents. Enzyme. Microb. Technol. 2001, 29: 129-135.
[23] Chopineau J, Mccafferty FD, Therisod M, et al. Production of biosurfactants from sugar alcohols and vegetable oils catalyzed by lipases in a nonaqueous media. Biotechnol. Bioengin. 1988, 31: 208-214.
[24] Margolin AL, Fitzpatrick PA, Dubin PL, et al. Chemenzymatic synthesis of optically active (meth) acrylic polymers. J. Am. Chem. Soc. 1991, 4693-4693.
[25] Gill I, Valivety R. Polyunsaturated fatty acids :Part 1. Occurrence, biological activities and applications. Trends. Biotechnol.1997,15: 401-409.
[26] Verger R. Interfacial activation of lipases: facts and artifacts. Trends. Biotechnol. 1997, 15: 32–38.
[27] Arpigny JL, Jaeger KE. Bacterial lipolytic enzymes:classification and properties. Biochem. J. 1999, 343: 177-183.
[28] Schmidt-Dannert C, Luisa Rfia M, Atomi H, Schmid RD. Biochim. Biophys. Acta. 1996, 1301: 05-114.
[29] Kim HK, Park SY, Lee JK, Oh TK. Biosci. Biotechnol. Biochem. 1998, 62: 66–71.
[30] Cho AR, Yoo SK, Kim EJ. FEMS. Microbiol. Lett. 2000, 186: 235–238.
[31] Sinchaikul S, Sookkheo B, Phutrakul S, Pan FM, Chen ST. Protein. Expres. Purif. 2001, 22: 388-398.
[32] Abdel-Fattah YR, Gaballa AA. Identification and over-expression of a thermostable lipase from Geobacillus thermoleovorans Toshki in Escherichia coli. Microbiol. Res. 2008, 163: 13-20.
[33] Leow TC, Rahman RN, Basri M, Salleh AB. A thermoalkaliphilic lipase of Geobacillus sp. T1. Extremophiles. 2007, 11: 527-535.
[34] Quintana-Castro R, Díaz P, Valerio-Alfaro G, García HS, Oliart-Ros R. Gene cloning, expression and characterization of the Geobacillus Thermoleovorans CCR11 thermoalkaliphilic lipase. Mol. Biotechnol. 2009, 42: 75-83.
[35] Upton C, Buckley JT. A new family of lipolytic enzymes. Trends. Biochem. Sci. 1995, 20: 178–179.
[36] Dalrymple BP, Cybinski DH, Layton I, McSweeney CS, Xue GP, Swadling YJ, et al. Three Neocallimastix patriciarum esterases associated with the degradation of complex polysaccharides are members of a new family of hydrolases. Microbiology. 1997, 143: 2605–2614.
[37] Li J, Derewenda U, Dauter Z, Smith S, Derewenda ZS. Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme. Nat. Struct. Biol. 2000, 7: 555–559.
[38] Molgaard A, Kauppinen S, Larsen S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Struct. Fold. Des. 2000, 8: 373–383.
[39] Lo YC, Lin SC, Shaw JF, Liaw YC. Crystal structure of the Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network. J. Mol. Biol. 2003, 330: 539–551.
[40] Cho H, Cronan JE. Escherichia coli thioesterase I, molecular cloning and sequencing of the structural gene and identification as a periplasmic enzume. J. Biol. Chem. 1993, 268: 9238–9245.
[41] Koshland DE. Application of a theory of enzyme specificity to protein synthesis (in Symposium on Amino Acid Activation). Proc. Natl. Acad. Sci. USA. 1958, 44: 98-104.
[42] Cruz H, Perez C, Wellington E, Castro C, Servin-Gonzalez L. Sequence of the Streptomyces albus G lipase-encoding gene reveals the presence of a prokaryotic lipase family. Gene. 1994, 144: 141-142.
[43] Wei Y, Swenson L, Castro C, Derewenda U, Minor W, Arai H, Aoki J, Inoue K, Servin-Gonzalez L, Derewenda ZS. Structure of a microbial homologus of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution. Structure. 1998, 6: 511-519.
[44] Hemila H., Koivula TT, Palva I. Hormone-sensitive lipase is closely related to several bacterial proteins, and distantly related to acetylcholinesterase and lipoprotein lipase: identification of a superfamily of esterases and lipases. Biochim. Biophys. Acta 1994, 1210: 249-253.
[45] Manco G, Giosue E, D’Auria S, Herman P, Carrea G, and Rossi M. Cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon Archaeoglobus fulgidus. Arch. Biochem. Biophys. 2000, 373: 182–192.
[46] Kim SB, Lee W, Ryu YW. Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus. J. Microbiol. 2008, 46: 100-107.
[47] Morana A, Prizito ND, Aurilia V, Rossi M, Cannio R. Acarboxylesterase from the hyperthermophilic archaeon Sulfolobus solfataricus: cloning of the gene, characterization of the protein. Gene. 2002, 283: 107–115.
[48] Hotta Y, Ezaki S, Atomi H, Imanaka T. Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl. Environ. Microbiol. 2002, 68: 3925–3931.
[49] Mandrich L, Menchise V, Alterio V, De-Simone G, Pedone C, Rossi M, Manco G. Functional and structural features of the oxyanion hole in a themophilic esterase from Alicyclobacillus acidocaldarius. Proteins. 2007, 71: 1721-1731.
[50] Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 2005, 71: 817-825.
[51] Kim KK, Song HK, Shin DH, Hwang KY, Choe S, Yoo OJ, Suh SW. Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity. Structure. 1997, 5: 1571-1584.
[52] Hong KH, Jang WH, Choi KD, Yoo OJ. Characterization of Pseudomonasfluorescens carboxylesterase: cloning and expression of the esterase gene in Escherichia coli. Agric. Biol. Chem. 1991, 55: 2839-2845.
[53] Nishizawa M, Shimizu M, Ohkawa H, Kanaoka M. Appl. Environ. Microbiol. 1995, 61: 3208-3215.
[54] Lobkovsky E, Moews PC, Liu H, Zhao H, Fre' re JM, Knox JR. Stereoselective production of (+)-trans-chrysanthemic acid by a microbial esterase: cloning, nucleotide sequence, and overexpression of the esterase gene of Arthrobacter globiformis in Escherichia coli. Proc. Natl. Acad. Sci. USA. 1993, 90: 11257-11261.
[55] Kim YS, Lee HB, Choi KD, Park S, Yoo OJ. Cloning of Pseudomonas fluorescens carboxylesterase gene and characterization of its product expressed in Escherichia coli. Biosci. Biotechnol.Biochem. 1994, 58: 111-116.
[56] Handrick R, Reinhardt S, Focarete ML, Scandola M, Adamus G, Kowalczuk M, Jendrossek D. A new type of thermoalkalophilic hydrolase of Paucimonas lemoignei with high specificity for amorphous polyesters of short chain-length hydroxylalkanoic acids. J. Biol. Chem. 2001, 276: 36215–36224.
[57] Levisson M, Vander O, Kengen SWM. Characterization and structural modeling of a new type of thermostable esterase from Thermotoga maritima. FEBS. 2007, 274: 2832–2842.
[58] de Pascale D, Cusano AM, Autore F, Parrilli E, di Prisco G, Marino G, Tutino ML. The cold-active Lip1 lipase from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is a member of a new bacterial lipolytic enzyme family. Extremophiles. 2008. 12: 311–323.
[59] Rathi P, Bradoo S, Saxena RK, Gupta R. A hyper-thermostable alkaline lipase from Pseudomonas sp. with the property of thermal activation. Biotech. Lett. 2000, 22: 495-498.
[60] Kakugawa K, Shobayashi M, Suzuki O, Miyakawa T. Purification and characterization of a lipase from the glycolipid-producing yeast Kurtzmanomyces sp. l'11. Biosci. Biotechnol. Biochem. 2002, 66: 978-S85.
[61] Salameh MA, Wiegel J. Purification and characterization of two highly thermophilic alkaline lipases from Thermosyntropha lipolytica. Appl. Environ. Microbiol. 2007, 73: 7725-7731.
[62] Sobek H, Gorisch H. Further kinetic and molecular characterization of an extremely heat-stable carboxylesterase from the thermoacidophilic archaebacterium Sulfolobusacidocaldarius. Biochem. J. 1989, 261: 993–998.
[63] Ikeda M, Clark DS. Molecular cloning of extremely thermostable esterase gene from hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli. Biotechnol Bioeng. 1998, 57: 624–629.
[64] Huddleston S, Yallop CA, Charalambous BM. The identification and partial characterisation of a novel inducible extracellular thermostable esterase from the archaeon Sulfolobus shibatae. Biochem. Biophys. Res. Commun. 1995, 216: 495-500.
[65] Noble MEM, Cleasby A, Johnson LN, Egmond MR, Frenken LGJ. The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic asparate. FEBS. Lett. 1993, 331: 123-28.
[66] Jaeger KE, Dijkstra BW, Reetz MT. Bacterial biocatalysts:molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol. 1999, 53: 315-351.
[67] Kim KK, Song HK, Shin DH, Hwang KY, Suh SW. The crystal of structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. Structure. 1997, 5: 173-185.
[68] Lang D, Hofmann B, Haalck L, Hecht HJ, Spener F, et al, Crystal sturcture of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6? resolution. J. Mol. Biol. 1996, 259: 704-714.
[69] Kim KK, Song HK, Shin DH, Hwang KY, Choe S, et al. Crystal of carboxylesterase from Pseudomonas fluorescens, anα/βhydrolase with broad substrate specificity. Structure. 1997, 5: 1571-1584.
[70] Aloulou A, Rodriguez JA, Fernandez S, Oosterhout DV, Puccinelli D, Carrere F. Exploring the specific features of interfacial enzymology based on lipase sudies. Biochimica. et Biophysica. Acta. 2006, 1761: 995-1013.
[71] Lesuisse E, Schanck K, Colson C. Purification and preliminary characterization of the extracellular lipase of Bacillus subtilis 168, an extremely basic pH tolerant enzyme. Eur. J. Biochem. 1993, 216: 155-160.
[72] Hjorth A, Carriere F, Cudrey C, Woldike H, Boel E, Lawson DM, Ferrato F, Cambillau C, Dodson GG, Thim L, Verger R. A structural domain (the Iid) found in pancreatic lipases is absent in the guinea pig (phospho) lipase. Biochemistry. 1993, 32: 4702-4707.
[73] Chen CK, Lee GC, Ko TP, Guo RT, Huang LM, Liu HJ, Ho YF, Shaw JF, Wang AH. Structure of the Alkalohyperthermophilic Archaeoglobus fulgidus Lipase Contains a Unique C-Terminal Domain Essential for Long-Chain Substrate Binding. J. Mol. Biol. 2009, 390: 672–685.
[74] Abedi Karjiban R, Abdul Rahman MB, Basri M, Salleh AB, Jacobs D, Abdul Wahab H. Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures. Protein. J. 2009, 28: 14–23.
[75] Tyndall JD, Sinchaikul S, Fothergill-Gilmore LA, Taylor P, Walkinshaw MD. Crystal Structure of a Thermostable Lipase from Bacillus stearothermophilus P1. J. Mol. Biol. 2002, 323: 859–869.
[76] Matsumura H, Yamamoto T, Leow TC, Mori T, Salleh AB, Basri M, Inoue T, Kai Y, Rahman RN. Novel cation-πinteraction revealed by crystal structure of thermoalkalophilic lipase. Proteins. 70: 592-598.
[77] Jaeger KE, Dijkstra BW, Reetz MT. Bacterial biocatalysis: Molecular biology, three-dimensional structures and biotechnological applications of lipases. Annu. Rev. Microbiol. 1999, 53: 315-351.
[78] Jaeger KE, Ransac S, Dijkstra BW, Colson C, van Heuvel M, Misset O. Bacterial lipases. Microbiol. Rev. 1994, 15: 29-63.
[79] Derewenda U, Swenson L, Green R, WeiY, Dodson GG, et al. An unusual buried polar cluster in a family of fungal lipases. Nat. Struct. Biol. 1994, 1: 36-47.
[80] Egloff M-P, Marguet F, Buono G, Verger R, Cambillau C, et al. The 2.46? resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate. Biochemistry. 1995. 34: 2751–62.
[81] Grochulski P, Bouthillier F, Kazlauskas RJ, Serreqi AN, Schrag JD, Ziomek E, Cygler M. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry. 1994, 33: 3494-500.
[82] Lang DA, Mannesse MLM, de Haas GH, Verheij HM, Dijkstra BW. Structural basis of the chiral selectivity of Pseudomonas cepacia lipase. Eur. J. Biochem. 1998, 254: 333-40.
[83] Longhi S, Verheij HM, deHaas GH, Egmond M, et al. Crystal structure of cutinase covalently inhibited by a triglyceride analogue. Protein. Sci. 1997, 6: 275-86.
[84] Sarda L, Desnuelle P. Actions of pancreatic lipase on esters in emulsions. Biochim. Biophys. Acta. 1958, 30: 513–21.
[85] Brzozowski AM, Derewenda U, Derewenda ZS, Dodson GG, Lawson DM, et al. A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature. 1991, 351: 491-94.
[86] Derewenda U, Brzozowski AM, Lawson DM, Derewenda ZS. Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase. Biochemistry. 1992, 31: 1532-41.
[87] van Tilbeurgh H, Egloff MP, Martinez C, Rugani N, Verger R, et al. Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography. Nature. 1993, 362: 814–20.
[88] Schrader G. Organische phosphor-verbindungen als neuartige insektizide (auszug). Angew. Chem. 1950, 62: 471-473.
[89] Dumas, DP, Durst HD, Landis WG, Raushel FM, Wild JR. Inactivation of organophosphorus nerve agents by the phosphotriesterase from Pseudomonas diminuta. Arch. Biochem. Biophys. 1990b, 277: 155-159.
[90] Kolakowski JE, DeFrank JJ, Harvey SP, Szafraniec LL, Beaudry WT, Lai K, Wild JR. Enzymatic hydrolysis of the chemical warfare agent VX and its neurotoxic analogues by organophosphorus hydrolase. Biocatal. Biotransform. 1997, 15: 297-312.
[91] Afriat L, Roodveldt C, Manco G, Tawfik DS, The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry. 2006, 45: 13677–13686.
[92] Xiang DF, Kolb P, Fedorov A, Meier M, Fedorov E, Nguyen T, Sterner R, Almo S, Shoichet B, Raushel F. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry. 2009, 48: 2237–2247.
[93] Elias M, Dupuy J, Merone L, Mandrich L, Porzio E, Moniot S, Rochu D, Lecomte C, Rossi M, Masson P, Manco G, Chabriere E. Structural basis for natural lactonase and promiscuous phosphotriesterase activities. J. Mol. Biol. 2008, 379: 1017–1028.
[94] Holm L, Sander C, An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins. 1997, 28: 72– 78.
[95] Benning MM, Kuo JM, Raushel FM, Holden HM. Three dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents. Biochemistry. 1994, 33: 15001-15007.
[96] Omburo GA, Kuo JM, Mullins LS, Raushel FM. Characterization of the zinc binding site of bacterial phosphotriesterase. J. Biol. Chem. 1992, 267: 13278–13283.
[97] Vanhooke JL, Benning MM, Raushel FM, Holden HM. Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry. 1996, 35: 6020-6025.
[98] Benning MM, Hong SB, Raushel FM, Holden HM. The binding of substrate analogs to phosphotriesterase. J. Biol. Chem. 2000, 275: 30556-305600.
[99] Merone L, Mandrich L, Rossi M, Manco G. A thermostable phosphotriesterase from the archaeon Sulfolobus solfataricus: cloning, overexpression and properties. Extremophiles. 2005, 9: 297-305.
[100] Rochu D, Viguie N, Renault F, Crouzier D, Froment MT, Patrick M. Biochem. J. 2004, 15: 627–633.
[101] Hawwa R, Larsen SD, Ratia K, Mesecar AD. Structure-based and random mutagenesis approaches increase the organophosphate-degrading activity of a phosphotriesterase homologue from Deinococcus radiodurans. J. Mol. Biol. 2009, 393: 36-57.
[102] Hawwa R, Aikens J, Turner RJ, Santarsiero BD, Mesecar AD. Structural basis for thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus. Arch. Biochem. Biophys. 2009, 488: 109-120.
[103] Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation forhomologous proteins using an energy-based rotamer seareh. J. Mol. Biol. 1993,229(4): 996-1006.
[104] Vasquez M. Modeling side-chain conformation. Curr. Opin. Struct. Biol. 1996,6(2): 217-21.
[105] Koehl P, Levitt M. A brighter future for Protein strueture Predietion. Nat. Struet. Biol. 1999, 6(2):108-111.
[106] John B, Sali A. Comparative Protein structure modeling by iterative aligment,model building and model assessment. Nucleie. Acids. Res. 2003, 31(14):3982-92.
[107] Ginalski K.Comparative modeling for Protein structure Predietion. Curr Opin Struct Biol, 2006, 16(2):172-7.
[108] Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional sturcture. Science. 1991, 253(5016): 164-70.
[109] Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recgnition. Nature. 1992, 358(6381): 86-89.
[110] Rost B. Schneider R, Sander C. Protein fold recognition by prediction-based threading. J. Mol. Biol. 1997, 270(3): 471-80.
[111] Rice DW. Eisenberg D. A 3D-1D substitution marix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol, 1997, 267(4): 1026-38.
[112] Ding CH. Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics. 2001, 17(4): 349-58.
[113] Zhang Y. 1-TASSER server for protein 3D structure prediction. BMC. Bioinformatics. 2008, 9: 40.
[114] Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins. 2001, 45: 39-46.
[115] Kelley LA, Sternberg MJE. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4: 363-71.
[116] Gustiananda M, Liggins JR, Cummins PL, Gready JE. Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations. Biophys. J. 2004, 86: 2467-83.
[117] Sonoda MT, Moreira NH, Martinez L. A Review on the Dynamics of Water, Braz. J.Phys. 2004, 34: 3-16.
[118] Michael L. The birth of computational structural biology, Nat. Struct. Mol. Biol. 2001, 8: 392-393.
[119] Weiner PW, Kollman PA.AMBER: assisted model building with energy refinement. A general program for modelling moleculars and their interactions. J. Comput. Chem. 1981, 2: 287-303.
[120] Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 1999, 103: 3596-3607.
[121] Tuckerman ME, Martyna GJ. Understanding modern molecular dynamics methods. J. Phys. Chem. 2000, 104: 159.
[122] van Gunsteren WF, Weiner PK, Wilkinson AJ. Theoretical and Experimental Applications Vol. 2, 1993, ESCOM, Leiden.
[123] Becker OM, MacKerell AD, Jr Roux B, Watanabe M. Computational Biochemistry and Biophysics. 2001, Marcel Dekker.
[124] Hayward S, Kitao A, Go N. Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins: Struct. Funct. Genet. 1995, 23:177-186.
[125] Zaloj V, Elber R. Parallel computations of molecular dynamics trajectories using the stochastic path approach. Comput. Phys. Commun. 2000, 128: 118-27.
[126] Lamb ML, Jorgenson W. Computational approaches to molecular recognition. Curr. Opin. Struct. Biol. 1997, 1: 449-457.
[127] Kollman P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93: 2395-2417.
[128] van Gunsteren WF, Mark AE. Validation of molecular dynamics simulation. J. Chem. Phys. 1998, 108: 6109.
[129] Gao JL, Truhlar DG. Quantum mechanical methods for enzyme kinetics. Annu. Rev. Phys. Chem. 2002, 53: 467-505.
[130] Pantazatos D, Kim JS, Kolck HE, et al. Rapid refinement ofcrystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. USA, 2004, 101(3): 751-756
[131]蛋白质结构研究方法进展。科学热点[Z]。江南大学图书馆情报部,2006,(2)。
[132] Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch. Microbiol. 1984, 141: 63-69.
[1] Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24: 1596–1599.
[2] Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch. Microbiol. 1984, 141: 63-69.
[3] Dharmsthiti S, Pratuangdejkul J, Theeragool GT, Luchai S. Lipase activity and gene cloning of Acinetobacter calcoaceticus LP009. Gen. J. Appl. Microbiol. 1998, 44: 139-145.
[4] Gao RJ, Feng Y, Ishikawa K, Ishida H, Ando S, Kosugi Y, Cao SG. Cloning, purification and properties of a hyperthermophilic esterase from archaeon Aeropyrumpernix K1. J. Mol. Catal. B: Enzym. 2003, 24/25:1–8.
[5] Juhasz T, Szeltner Z, Polgar L. Properties of the prolyl oligopeptidase homologue from Pyrococcus furiosus. FEBS Lett. 2006. 580: 3493-3497.
[6] Hun CJ, Zaliha RN, Rahman A, Salleh AB, Basri M. A newly isolated organic solvent tolerant Bacillus sphaericus 205y producing organic solvent-stable lipase. Biochem. Eng. J. 2003, 15: 147–151.
[7] Ogino H, Ishikawa H. Enzymes which are stable in the presence of organic solvents. J. Biosci. Bioeng. 2001, 91: 109–116.
[8] Sellek GA, Chaudhuri JB. Biocatalysis in organic media using enzymes from extramophiles. Enzyme. Microbiol. Technol. 1999, 25: 471-482.
[9] Klibanov AM. Improving enzymes by using them in organic solvents. Nature. 2001, 409: 241-246.
[10] Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic program 3D-JIGSAW and 3D-PSSM. Proteins 2001, 45: 39-46.
[11] Kelley LA, Sternberg MJE. Protein structure prediction on the web: a case study using the Phyre server. Nat. Protoc. 2009, 4: 363-71.
[12] Case DA, Darden TA, Cheatham TEIII, Simmerling CL, et al. University of California, San Francisco.2006.
[13] Trodler P, Schmid RD, Pleiss J. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct. Biol. 2009, 9: 38.
[14] Ryckaert J-P, Ciccotti G., Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constrains: molecular dynamics of n-alkanes J. Computat. Phys. 1977, 23: 327–341.
[15] Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992, 356: 83-85.
[16] Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993, 26: 283-291.
[17] Huey R, Morris GM, Olson AJ, Goodsell DH. A semi-empirical free energy force field with charge-based desolvation. J. Comput. Chem. 2007, 28: 1145-1152.
[18] De Oliveira EB, Humeau C, Chebil L, Maia ER, Dehez F, Maigret B, Ghoul M, Engasser JM. A molecular modelling study to rationalize the regioselectivity in acylation of flavonoid glycosides catalyzed by Candida antarctica lipase B. J. Mol. Catal. B: Enzym. 2009, 59: 96-105.
[19] Williams DH, Stephens E, OBrien DP, Zhou M. Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes. Angew. Chem. Int. Ed. 2004, 43: 6596-6616.
[20] Veld MAJ, Fransson L, Palmans ARA, Meijer EW, Hult K. Lactone size dependent reactivity in Candida antarctica lipase B: A molecular dynamics and docking study. ChemBioChem. 2009, 10: 1330-1334.
[21] Svedendahl M, Carlqvist P, Branneby C, Allner O, Frise A, Hult K, Berglund P, Brinck T. Direct Epoxidation in Candida antarctica Lipase B Studied by Experiment and Theory. ChemBioChem. 2008, 9: 2443-2451.
[1] Manco G, Giosue E, D’Auria S, Herman P, Carrea G, and Rossi M. Cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon Archaeoglobus fulgidus. Arch. Biochem. Biophys. 2000, 373: 182–192.
[2] Kim SB, Lee W, Ryu YW. Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus. J. Microbiol. 2008, 46: 100-107.
[3] Morana A, Prizito ND, Aurilia V, Rossi M, Cannio R. Acarboxylesterase from the hyperthermophilic archaeon Sulfolobus solfataricus: cloning of the gene, characterization of the protein. Gene. 2002, 283:107–115.
[4] Hotta Y, Ezaki S, Atomi H, Imanaka T. Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl. Environ. Microbiol. 2002, 68: 3925–3931.
[5] Mandrich L, Menchise V, Alterio V, De-Simone G, Pedone C, Rossi M, Manco G. Functional and structural features of the oxyanion hole in a themophilic esterase from Alicyclobacillus acidocaldarius. Proteins. 2007, 71: 1721-1731.
[6] Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 2005, 71: 817-825.
[7] Matthias H, Moritz K, Garabed A. Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. Extremophiles. 2008, 12: 351-364.
[1] Dumas DP, Caldwell SR, Wild JR, Raushel FM. Purification and properties of the phosphotriesterase from Pseudomonas diminuta. J. Biol. Chem. 1989. 264(33): 19659-65.
[2] Hawwa R, Aikens J, Turner RJ, Santarsiero BD, Mesecar AD. Structural basis of thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus. Arch. Biochem. Biophys. 2009, 488: 109-120.
[3] Larsen S, Ratia K, Santarsiero B, Mesecar A. Monochromatic and Polychromatic Laue Studies of a Novel Phosphotriesterase that Degrades Soman Gas, Midwest Enzyme Chemistry Conference XXIII, University of Illinois at Chicago, 2003.
[4] Benning MM, Kuo JM, Raushel FM, Holden HM. Three-dimensional structure of the binuclear metal center of phosphotriesterase. Biochemistry, 1995, 34: 7973-8.
[5] Elias M, Dupuy J, Merone L, Mandrich L, Porzio E, Moniot S, Rochu D, Lecomte C, Rossi M, Masson P, Manco G, Chabriere E. Structural basis for natural lactonase and promiscuous phosphotriesterase activities. J. Mol. Biol. 2008, 379: 1017-28.
[6] Aloulou A., Rodriguez JA, Fernandez S, Oosterhout DV, Puccinelli D, Carrere F. Exploring the specific features of interfacial enzymology based on lipase sudies. BBA. 2006, 1761:995-1013.
[2] Rothschild LJ, Mancinelli RL. Life in extreme environ- ments. Nature. 2001, 409: 1092-1101.
[3] Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and EucaryaProc. Nati. Acad. Sci. USA. 1990, 87: 4576-4579.
[4] James RB, Andrei NL. What makes a thermophile. Trends in Microbiology. 1998, 6: 349-351.
[5] Palackal N, Brennan Y, Callen WN, Dupree P, Frey G, Goubet F, Hazlewood GP, Healey S, Kang YE, Kretz KA, et al: An evolutionary route to xylanase process fitness. Protein. Sci. 2004, 13: 494-503.
[6] Cowan DA: Thermophilic proteins: stability and function in aqueous and organic solvents. Comp. Biochem. Physiol. A. Physiol. 1997, 118: 429-438.
[7] Polizzi KM, Bommarius AS, Broering JM, Chaparro-Riggers JF. Stability of bilcatalysts. Curr. Opin. Chem. Biol. 2007, 11: 220-225.
[8] Demirjian DC, Morís-Varas F, Cassidy CS. Enzymes from extremophiles. Curr. Opin. Chem. Biol. 2001, 5: 144-151.
[9] Becker P. Determination of the kinetic parameters during continuous cultivation of the lipase producing thermophile Bacillus sp. IHI-91 on olive oil. Appl. Microb. Biotechnol. 1997, 48: 184–190.
[10] Mozhaev V. Mechanism-based strategies for protein thermostabilization. Trends. Biotechnol. 1993, 11: 88–95.
[11] Krahe M, Antranikian G, Markel H. Fermentation of extremophilic microorganisms. FEMS. Microbiol. Rev. 1996, 18: 271–285.
[12] Kumar S, Nussinov R. How do thermophilic proteins deal with heat? A review. Cell. Mol. Life Sci. 2001, 58: 1216–1233.
[13]林影,卢嶸德。极端酶及其工业应用。工业微生物。2000, 30(2): 51-53。
[14] Haki GD, Rakshit SK. Developments in industrially important thermostable enzymes: a review. Bioresour. Technol. 2003, 89(1): 17-34.
[15] Batto M, Mathrani IM, Ahringb, et al. Appl. micobiol. Biotech. 1994, 41: 130-133.
[16] Bartolucci S, Rella R, Guagliardi A, Raia CA, Gambacorta A, Rosa MD, Rossi M. Malic enzyme from archaebacterium Sulfolobus solfataricus: purification, structure, and kinetic properties. J. Biol. Chem. 1987, 262: 7725-7731.
[17] Klug MJ, Markovetz AJ. Thermophilic bacterium isolated on n-tetradecane. Nature. 1967, 215: 1082-1083.
[18] Kargi F, Robinson JM. Removal of sulfur compounds from coal by the thermophilic organism sulfolobus acidocaldarius. Appl. Environ. Microbiol. 1982, 44: 878-883.
[19] McCutchen CM, Duffaud GD, Leduc P, Petersen AR, Tayal A, Khan SA, Kelly RM.. Characterization of extremely thermostable enzymatic breakers (alpha-1,6-galactosidase and beta-1,4-mannanase) from the hyperthemophilic bacterium Thermotoga neapolitana 5068 for hydrolysis of guar gum. Biltechnol. Bioent. 1996, 52: 332-339.
[20] IUPAC-IUB commission on nomenlature, enzyme nomenclature, academic press, New York. 1979, P6.
[21] Undurraga D, Markovits A, Erazo S. Cocoa butter equivalent through enzymic interesterification of palmoil midfraction. Process. Biochem. 2001, 36: 933-939.
[22] Zhang LQ, Zhang YD, Xu L, et al. Lipase catalyzed synthesis of RGD diamide in aqueous water-miscible organic solvents. Enzyme. Microb. Technol. 2001, 29: 129-135.
[23] Chopineau J, Mccafferty FD, Therisod M, et al. Production of biosurfactants from sugar alcohols and vegetable oils catalyzed by lipases in a nonaqueous media. Biotechnol. Bioengin. 1988, 31: 208-214.
[24] Margolin AL, Fitzpatrick PA, Dubin PL, et al. Chemenzymatic synthesis of optically active (meth) acrylic polymers. J. Am. Chem. Soc. 1991, 4693-4693.
[25] Gill I, Valivety R. Polyunsaturated fatty acids :Part 1. Occurrence, biological activities and applications. Trends. Biotechnol.1997,15: 401-409.
[26] Verger R. Interfacial activation of lipases: facts and artifacts. Trends. Biotechnol. 1997, 15: 32–38.
[27] Arpigny JL, Jaeger KE. Bacterial lipolytic enzymes:classification and properties. Biochem. J. 1999, 343: 177-183.
[28] Schmidt-Dannert C, Luisa Rfia M, Atomi H, Schmid RD. Biochim. Biophys. Acta. 1996, 1301: 05-114.
[29] Kim HK, Park SY, Lee JK, Oh TK. Biosci. Biotechnol. Biochem. 1998, 62: 66–71.
[30] Cho AR, Yoo SK, Kim EJ. FEMS. Microbiol. Lett. 2000, 186: 235–238.
[31] Sinchaikul S, Sookkheo B, Phutrakul S, Pan FM, Chen ST. Protein. Expres. Purif. 2001, 22: 388-398.
[32] Abdel-Fattah YR, Gaballa AA. Identification and over-expression of a thermostable lipase from Geobacillus thermoleovorans Toshki in Escherichia coli. Microbiol. Res. 2008, 163: 13-20.
[33] Leow TC, Rahman RN, Basri M, Salleh AB. A thermoalkaliphilic lipase of Geobacillus sp. T1. Extremophiles. 2007, 11: 527-535.
[34] Quintana-Castro R, Díaz P, Valerio-Alfaro G, García HS, Oliart-Ros R. Gene cloning, expression and characterization of the Geobacillus Thermoleovorans CCR11 thermoalkaliphilic lipase. Mol. Biotechnol. 2009, 42: 75-83.
[35] Upton C, Buckley JT. A new family of lipolytic enzymes. Trends. Biochem. Sci. 1995, 20: 178–179.
[36] Dalrymple BP, Cybinski DH, Layton I, McSweeney CS, Xue GP, Swadling YJ, et al. Three Neocallimastix patriciarum esterases associated with the degradation of complex polysaccharides are members of a new family of hydrolases. Microbiology. 1997, 143: 2605–2614.
[37] Li J, Derewenda U, Dauter Z, Smith S, Derewenda ZS. Crystal structure of the Escherichia coli thioesterase II, a homolog of the human Nef binding enzyme. Nat. Struct. Biol. 2000, 7: 555–559.
[38] Molgaard A, Kauppinen S, Larsen S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Struct. Fold. Des. 2000, 8: 373–383.
[39] Lo YC, Lin SC, Shaw JF, Liaw YC. Crystal structure of the Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network. J. Mol. Biol. 2003, 330: 539–551.
[40] Cho H, Cronan JE. Escherichia coli thioesterase I, molecular cloning and sequencing of the structural gene and identification as a periplasmic enzume. J. Biol. Chem. 1993, 268: 9238–9245.
[41] Koshland DE. Application of a theory of enzyme specificity to protein synthesis (in Symposium on Amino Acid Activation). Proc. Natl. Acad. Sci. USA. 1958, 44: 98-104.
[42] Cruz H, Perez C, Wellington E, Castro C, Servin-Gonzalez L. Sequence of the Streptomyces albus G lipase-encoding gene reveals the presence of a prokaryotic lipase family. Gene. 1994, 144: 141-142.
[43] Wei Y, Swenson L, Castro C, Derewenda U, Minor W, Arai H, Aoki J, Inoue K, Servin-Gonzalez L, Derewenda ZS. Structure of a microbial homologus of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution. Structure. 1998, 6: 511-519.
[44] Hemila H., Koivula TT, Palva I. Hormone-sensitive lipase is closely related to several bacterial proteins, and distantly related to acetylcholinesterase and lipoprotein lipase: identification of a superfamily of esterases and lipases. Biochim. Biophys. Acta 1994, 1210: 249-253.
[45] Manco G, Giosue E, D’Auria S, Herman P, Carrea G, and Rossi M. Cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon Archaeoglobus fulgidus. Arch. Biochem. Biophys. 2000, 373: 182–192.
[46] Kim SB, Lee W, Ryu YW. Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus. J. Microbiol. 2008, 46: 100-107.
[47] Morana A, Prizito ND, Aurilia V, Rossi M, Cannio R. Acarboxylesterase from the hyperthermophilic archaeon Sulfolobus solfataricus: cloning of the gene, characterization of the protein. Gene. 2002, 283: 107–115.
[48] Hotta Y, Ezaki S, Atomi H, Imanaka T. Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl. Environ. Microbiol. 2002, 68: 3925–3931.
[49] Mandrich L, Menchise V, Alterio V, De-Simone G, Pedone C, Rossi M, Manco G. Functional and structural features of the oxyanion hole in a themophilic esterase from Alicyclobacillus acidocaldarius. Proteins. 2007, 71: 1721-1731.
[50] Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 2005, 71: 817-825.
[51] Kim KK, Song HK, Shin DH, Hwang KY, Choe S, Yoo OJ, Suh SW. Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity. Structure. 1997, 5: 1571-1584.
[52] Hong KH, Jang WH, Choi KD, Yoo OJ. Characterization of Pseudomonasfluorescens carboxylesterase: cloning and expression of the esterase gene in Escherichia coli. Agric. Biol. Chem. 1991, 55: 2839-2845.
[53] Nishizawa M, Shimizu M, Ohkawa H, Kanaoka M. Appl. Environ. Microbiol. 1995, 61: 3208-3215.
[54] Lobkovsky E, Moews PC, Liu H, Zhao H, Fre' re JM, Knox JR. Stereoselective production of (+)-trans-chrysanthemic acid by a microbial esterase: cloning, nucleotide sequence, and overexpression of the esterase gene of Arthrobacter globiformis in Escherichia coli. Proc. Natl. Acad. Sci. USA. 1993, 90: 11257-11261.
[55] Kim YS, Lee HB, Choi KD, Park S, Yoo OJ. Cloning of Pseudomonas fluorescens carboxylesterase gene and characterization of its product expressed in Escherichia coli. Biosci. Biotechnol.Biochem. 1994, 58: 111-116.
[56] Handrick R, Reinhardt S, Focarete ML, Scandola M, Adamus G, Kowalczuk M, Jendrossek D. A new type of thermoalkalophilic hydrolase of Paucimonas lemoignei with high specificity for amorphous polyesters of short chain-length hydroxylalkanoic acids. J. Biol. Chem. 2001, 276: 36215–36224.
[57] Levisson M, Vander O, Kengen SWM. Characterization and structural modeling of a new type of thermostable esterase from Thermotoga maritima. FEBS. 2007, 274: 2832–2842.
[58] de Pascale D, Cusano AM, Autore F, Parrilli E, di Prisco G, Marino G, Tutino ML. The cold-active Lip1 lipase from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 is a member of a new bacterial lipolytic enzyme family. Extremophiles. 2008. 12: 311–323.
[59] Rathi P, Bradoo S, Saxena RK, Gupta R. A hyper-thermostable alkaline lipase from Pseudomonas sp. with the property of thermal activation. Biotech. Lett. 2000, 22: 495-498.
[60] Kakugawa K, Shobayashi M, Suzuki O, Miyakawa T. Purification and characterization of a lipase from the glycolipid-producing yeast Kurtzmanomyces sp. l'11. Biosci. Biotechnol. Biochem. 2002, 66: 978-S85.
[61] Salameh MA, Wiegel J. Purification and characterization of two highly thermophilic alkaline lipases from Thermosyntropha lipolytica. Appl. Environ. Microbiol. 2007, 73: 7725-7731.
[62] Sobek H, Gorisch H. Further kinetic and molecular characterization of an extremely heat-stable carboxylesterase from the thermoacidophilic archaebacterium Sulfolobusacidocaldarius. Biochem. J. 1989, 261: 993–998.
[63] Ikeda M, Clark DS. Molecular cloning of extremely thermostable esterase gene from hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli. Biotechnol Bioeng. 1998, 57: 624–629.
[64] Huddleston S, Yallop CA, Charalambous BM. The identification and partial characterisation of a novel inducible extracellular thermostable esterase from the archaeon Sulfolobus shibatae. Biochem. Biophys. Res. Commun. 1995, 216: 495-500.
[65] Noble MEM, Cleasby A, Johnson LN, Egmond MR, Frenken LGJ. The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic asparate. FEBS. Lett. 1993, 331: 123-28.
[66] Jaeger KE, Dijkstra BW, Reetz MT. Bacterial biocatalysts:molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol. 1999, 53: 315-351.
[67] Kim KK, Song HK, Shin DH, Hwang KY, Suh SW. The crystal of structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. Structure. 1997, 5: 173-185.
[68] Lang D, Hofmann B, Haalck L, Hecht HJ, Spener F, et al, Crystal sturcture of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6? resolution. J. Mol. Biol. 1996, 259: 704-714.
[69] Kim KK, Song HK, Shin DH, Hwang KY, Choe S, et al. Crystal of carboxylesterase from Pseudomonas fluorescens, anα/βhydrolase with broad substrate specificity. Structure. 1997, 5: 1571-1584.
[70] Aloulou A, Rodriguez JA, Fernandez S, Oosterhout DV, Puccinelli D, Carrere F. Exploring the specific features of interfacial enzymology based on lipase sudies. Biochimica. et Biophysica. Acta. 2006, 1761: 995-1013.
[71] Lesuisse E, Schanck K, Colson C. Purification and preliminary characterization of the extracellular lipase of Bacillus subtilis 168, an extremely basic pH tolerant enzyme. Eur. J. Biochem. 1993, 216: 155-160.
[72] Hjorth A, Carriere F, Cudrey C, Woldike H, Boel E, Lawson DM, Ferrato F, Cambillau C, Dodson GG, Thim L, Verger R. A structural domain (the Iid) found in pancreatic lipases is absent in the guinea pig (phospho) lipase. Biochemistry. 1993, 32: 4702-4707.
[73] Chen CK, Lee GC, Ko TP, Guo RT, Huang LM, Liu HJ, Ho YF, Shaw JF, Wang AH. Structure of the Alkalohyperthermophilic Archaeoglobus fulgidus Lipase Contains a Unique C-Terminal Domain Essential for Long-Chain Substrate Binding. J. Mol. Biol. 2009, 390: 672–685.
[74] Abedi Karjiban R, Abdul Rahman MB, Basri M, Salleh AB, Jacobs D, Abdul Wahab H. Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures. Protein. J. 2009, 28: 14–23.
[75] Tyndall JD, Sinchaikul S, Fothergill-Gilmore LA, Taylor P, Walkinshaw MD. Crystal Structure of a Thermostable Lipase from Bacillus stearothermophilus P1. J. Mol. Biol. 2002, 323: 859–869.
[76] Matsumura H, Yamamoto T, Leow TC, Mori T, Salleh AB, Basri M, Inoue T, Kai Y, Rahman RN. Novel cation-πinteraction revealed by crystal structure of thermoalkalophilic lipase. Proteins. 70: 592-598.
[77] Jaeger KE, Dijkstra BW, Reetz MT. Bacterial biocatalysis: Molecular biology, three-dimensional structures and biotechnological applications of lipases. Annu. Rev. Microbiol. 1999, 53: 315-351.
[78] Jaeger KE, Ransac S, Dijkstra BW, Colson C, van Heuvel M, Misset O. Bacterial lipases. Microbiol. Rev. 1994, 15: 29-63.
[79] Derewenda U, Swenson L, Green R, WeiY, Dodson GG, et al. An unusual buried polar cluster in a family of fungal lipases. Nat. Struct. Biol. 1994, 1: 36-47.
[80] Egloff M-P, Marguet F, Buono G, Verger R, Cambillau C, et al. The 2.46? resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate. Biochemistry. 1995. 34: 2751–62.
[81] Grochulski P, Bouthillier F, Kazlauskas RJ, Serreqi AN, Schrag JD, Ziomek E, Cygler M. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. Biochemistry. 1994, 33: 3494-500.
[82] Lang DA, Mannesse MLM, de Haas GH, Verheij HM, Dijkstra BW. Structural basis of the chiral selectivity of Pseudomonas cepacia lipase. Eur. J. Biochem. 1998, 254: 333-40.
[83] Longhi S, Verheij HM, deHaas GH, Egmond M, et al. Crystal structure of cutinase covalently inhibited by a triglyceride analogue. Protein. Sci. 1997, 6: 275-86.
[84] Sarda L, Desnuelle P. Actions of pancreatic lipase on esters in emulsions. Biochim. Biophys. Acta. 1958, 30: 513–21.
[85] Brzozowski AM, Derewenda U, Derewenda ZS, Dodson GG, Lawson DM, et al. A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex. Nature. 1991, 351: 491-94.
[86] Derewenda U, Brzozowski AM, Lawson DM, Derewenda ZS. Catalysis at the interface: the anatomy of a conformational change in a triglyceride lipase. Biochemistry. 1992, 31: 1532-41.
[87] van Tilbeurgh H, Egloff MP, Martinez C, Rugani N, Verger R, et al. Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography. Nature. 1993, 362: 814–20.
[88] Schrader G. Organische phosphor-verbindungen als neuartige insektizide (auszug). Angew. Chem. 1950, 62: 471-473.
[89] Dumas, DP, Durst HD, Landis WG, Raushel FM, Wild JR. Inactivation of organophosphorus nerve agents by the phosphotriesterase from Pseudomonas diminuta. Arch. Biochem. Biophys. 1990b, 277: 155-159.
[90] Kolakowski JE, DeFrank JJ, Harvey SP, Szafraniec LL, Beaudry WT, Lai K, Wild JR. Enzymatic hydrolysis of the chemical warfare agent VX and its neurotoxic analogues by organophosphorus hydrolase. Biocatal. Biotransform. 1997, 15: 297-312.
[91] Afriat L, Roodveldt C, Manco G, Tawfik DS, The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry. 2006, 45: 13677–13686.
[92] Xiang DF, Kolb P, Fedorov A, Meier M, Fedorov E, Nguyen T, Sterner R, Almo S, Shoichet B, Raushel F. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry. 2009, 48: 2237–2247.
[93] Elias M, Dupuy J, Merone L, Mandrich L, Porzio E, Moniot S, Rochu D, Lecomte C, Rossi M, Masson P, Manco G, Chabriere E. Structural basis for natural lactonase and promiscuous phosphotriesterase activities. J. Mol. Biol. 2008, 379: 1017–1028.
[94] Holm L, Sander C, An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins. 1997, 28: 72– 78.
[95] Benning MM, Kuo JM, Raushel FM, Holden HM. Three dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents. Biochemistry. 1994, 33: 15001-15007.
[96] Omburo GA, Kuo JM, Mullins LS, Raushel FM. Characterization of the zinc binding site of bacterial phosphotriesterase. J. Biol. Chem. 1992, 267: 13278–13283.
[97] Vanhooke JL, Benning MM, Raushel FM, Holden HM. Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate. Biochemistry. 1996, 35: 6020-6025.
[98] Benning MM, Hong SB, Raushel FM, Holden HM. The binding of substrate analogs to phosphotriesterase. J. Biol. Chem. 2000, 275: 30556-305600.
[99] Merone L, Mandrich L, Rossi M, Manco G. A thermostable phosphotriesterase from the archaeon Sulfolobus solfataricus: cloning, overexpression and properties. Extremophiles. 2005, 9: 297-305.
[100] Rochu D, Viguie N, Renault F, Crouzier D, Froment MT, Patrick M. Biochem. J. 2004, 15: 627–633.
[101] Hawwa R, Larsen SD, Ratia K, Mesecar AD. Structure-based and random mutagenesis approaches increase the organophosphate-degrading activity of a phosphotriesterase homologue from Deinococcus radiodurans. J. Mol. Biol. 2009, 393: 36-57.
[102] Hawwa R, Aikens J, Turner RJ, Santarsiero BD, Mesecar AD. Structural basis for thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus. Arch. Biochem. Biophys. 2009, 488: 109-120.
[103] Wilson C, Gregoret LM, Agard DA. Modeling side-chain conformation forhomologous proteins using an energy-based rotamer seareh. J. Mol. Biol. 1993,229(4): 996-1006.
[104] Vasquez M. Modeling side-chain conformation. Curr. Opin. Struct. Biol. 1996,6(2): 217-21.
[105] Koehl P, Levitt M. A brighter future for Protein strueture Predietion. Nat. Struet. Biol. 1999, 6(2):108-111.
[106] John B, Sali A. Comparative Protein structure modeling by iterative aligment,model building and model assessment. Nucleie. Acids. Res. 2003, 31(14):3982-92.
[107] Ginalski K.Comparative modeling for Protein structure Predietion. Curr Opin Struct Biol, 2006, 16(2):172-7.
[108] Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional sturcture. Science. 1991, 253(5016): 164-70.
[109] Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recgnition. Nature. 1992, 358(6381): 86-89.
[110] Rost B. Schneider R, Sander C. Protein fold recognition by prediction-based threading. J. Mol. Biol. 1997, 270(3): 471-80.
[111] Rice DW. Eisenberg D. A 3D-1D substitution marix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol, 1997, 267(4): 1026-38.
[112] Ding CH. Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics. 2001, 17(4): 349-58.
[113] Zhang Y. 1-TASSER server for protein 3D structure prediction. BMC. Bioinformatics. 2008, 9: 40.
[114] Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins. 2001, 45: 39-46.
[115] Kelley LA, Sternberg MJE. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4: 363-71.
[116] Gustiananda M, Liggins JR, Cummins PL, Gready JE. Conformation of prion protein repeat peptides probed by FRET measurements and molecular dynamics simulations. Biophys. J. 2004, 86: 2467-83.
[117] Sonoda MT, Moreira NH, Martinez L. A Review on the Dynamics of Water, Braz. J.Phys. 2004, 34: 3-16.
[118] Michael L. The birth of computational structural biology, Nat. Struct. Mol. Biol. 2001, 8: 392-393.
[119] Weiner PW, Kollman PA.AMBER: assisted model building with energy refinement. A general program for modelling moleculars and their interactions. J. Comput. Chem. 1981, 2: 287-303.
[120] Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 1999, 103: 3596-3607.
[121] Tuckerman ME, Martyna GJ. Understanding modern molecular dynamics methods. J. Phys. Chem. 2000, 104: 159.
[122] van Gunsteren WF, Weiner PK, Wilkinson AJ. Theoretical and Experimental Applications Vol. 2, 1993, ESCOM, Leiden.
[123] Becker OM, MacKerell AD, Jr Roux B, Watanabe M. Computational Biochemistry and Biophysics. 2001, Marcel Dekker.
[124] Hayward S, Kitao A, Go N. Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins: Struct. Funct. Genet. 1995, 23:177-186.
[125] Zaloj V, Elber R. Parallel computations of molecular dynamics trajectories using the stochastic path approach. Comput. Phys. Commun. 2000, 128: 118-27.
[126] Lamb ML, Jorgenson W. Computational approaches to molecular recognition. Curr. Opin. Struct. Biol. 1997, 1: 449-457.
[127] Kollman P. Free Energy Calculations: Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93: 2395-2417.
[128] van Gunsteren WF, Mark AE. Validation of molecular dynamics simulation. J. Chem. Phys. 1998, 108: 6109.
[129] Gao JL, Truhlar DG. Quantum mechanical methods for enzyme kinetics. Annu. Rev. Phys. Chem. 2002, 53: 467-505.
[130] Pantazatos D, Kim JS, Kolck HE, et al. Rapid refinement ofcrystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. USA, 2004, 101(3): 751-756
[131]蛋白质结构研究方法进展。科学热点[Z]。江南大学图书馆情报部,2006,(2)。
[132] Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch. Microbiol. 1984, 141: 63-69.
[1] Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24: 1596–1599.
[2] Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch. Microbiol. 1984, 141: 63-69.
[3] Dharmsthiti S, Pratuangdejkul J, Theeragool GT, Luchai S. Lipase activity and gene cloning of Acinetobacter calcoaceticus LP009. Gen. J. Appl. Microbiol. 1998, 44: 139-145.
[4] Gao RJ, Feng Y, Ishikawa K, Ishida H, Ando S, Kosugi Y, Cao SG. Cloning, purification and properties of a hyperthermophilic esterase from archaeon Aeropyrumpernix K1. J. Mol. Catal. B: Enzym. 2003, 24/25:1–8.
[5] Juhasz T, Szeltner Z, Polgar L. Properties of the prolyl oligopeptidase homologue from Pyrococcus furiosus. FEBS Lett. 2006. 580: 3493-3497.
[6] Hun CJ, Zaliha RN, Rahman A, Salleh AB, Basri M. A newly isolated organic solvent tolerant Bacillus sphaericus 205y producing organic solvent-stable lipase. Biochem. Eng. J. 2003, 15: 147–151.
[7] Ogino H, Ishikawa H. Enzymes which are stable in the presence of organic solvents. J. Biosci. Bioeng. 2001, 91: 109–116.
[8] Sellek GA, Chaudhuri JB. Biocatalysis in organic media using enzymes from extramophiles. Enzyme. Microbiol. Technol. 1999, 25: 471-482.
[9] Klibanov AM. Improving enzymes by using them in organic solvents. Nature. 2001, 409: 241-246.
[10] Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic program 3D-JIGSAW and 3D-PSSM. Proteins 2001, 45: 39-46.
[11] Kelley LA, Sternberg MJE. Protein structure prediction on the web: a case study using the Phyre server. Nat. Protoc. 2009, 4: 363-71.
[12] Case DA, Darden TA, Cheatham TEIII, Simmerling CL, et al. University of California, San Francisco.2006.
[13] Trodler P, Schmid RD, Pleiss J. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct. Biol. 2009, 9: 38.
[14] Ryckaert J-P, Ciccotti G., Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constrains: molecular dynamics of n-alkanes J. Computat. Phys. 1977, 23: 327–341.
[15] Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992, 356: 83-85.
[16] Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993, 26: 283-291.
[17] Huey R, Morris GM, Olson AJ, Goodsell DH. A semi-empirical free energy force field with charge-based desolvation. J. Comput. Chem. 2007, 28: 1145-1152.
[18] De Oliveira EB, Humeau C, Chebil L, Maia ER, Dehez F, Maigret B, Ghoul M, Engasser JM. A molecular modelling study to rationalize the regioselectivity in acylation of flavonoid glycosides catalyzed by Candida antarctica lipase B. J. Mol. Catal. B: Enzym. 2009, 59: 96-105.
[19] Williams DH, Stephens E, OBrien DP, Zhou M. Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes. Angew. Chem. Int. Ed. 2004, 43: 6596-6616.
[20] Veld MAJ, Fransson L, Palmans ARA, Meijer EW, Hult K. Lactone size dependent reactivity in Candida antarctica lipase B: A molecular dynamics and docking study. ChemBioChem. 2009, 10: 1330-1334.
[21] Svedendahl M, Carlqvist P, Branneby C, Allner O, Frise A, Hult K, Berglund P, Brinck T. Direct Epoxidation in Candida antarctica Lipase B Studied by Experiment and Theory. ChemBioChem. 2008, 9: 2443-2451.
[1] Manco G, Giosue E, D’Auria S, Herman P, Carrea G, and Rossi M. Cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon Archaeoglobus fulgidus. Arch. Biochem. Biophys. 2000, 373: 182–192.
[2] Kim SB, Lee W, Ryu YW. Cloning and characterization of thermostable esterase from Archaeoglobus fulgidus. J. Microbiol. 2008, 46: 100-107.
[3] Morana A, Prizito ND, Aurilia V, Rossi M, Cannio R. Acarboxylesterase from the hyperthermophilic archaeon Sulfolobus solfataricus: cloning of the gene, characterization of the protein. Gene. 2002, 283:107–115.
[4] Hotta Y, Ezaki S, Atomi H, Imanaka T. Extremely stable and versatile carboxylesterase from a hyperthermophilic archaeon. Appl. Environ. Microbiol. 2002, 68: 3925–3931.
[5] Mandrich L, Menchise V, Alterio V, De-Simone G, Pedone C, Rossi M, Manco G. Functional and structural features of the oxyanion hole in a themophilic esterase from Alicyclobacillus acidocaldarius. Proteins. 2007, 71: 1721-1731.
[6] Rhee JK, Ahn DG, Kim YG, Oh JW. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 2005, 71: 817-825.
[7] Matthias H, Moritz K, Garabed A. Extremely thermostable esterases from the thermoacidophilic euryarchaeon Picrophilus torridus. Extremophiles. 2008, 12: 351-364.
[1] Dumas DP, Caldwell SR, Wild JR, Raushel FM. Purification and properties of the phosphotriesterase from Pseudomonas diminuta. J. Biol. Chem. 1989. 264(33): 19659-65.
[2] Hawwa R, Aikens J, Turner RJ, Santarsiero BD, Mesecar AD. Structural basis of thermostability revealed through the identification and characterization of a highly thermostable phosphotriesterase-like lactonase from Geobacillus stearothermophilus. Arch. Biochem. Biophys. 2009, 488: 109-120.
[3] Larsen S, Ratia K, Santarsiero B, Mesecar A. Monochromatic and Polychromatic Laue Studies of a Novel Phosphotriesterase that Degrades Soman Gas, Midwest Enzyme Chemistry Conference XXIII, University of Illinois at Chicago, 2003.
[4] Benning MM, Kuo JM, Raushel FM, Holden HM. Three-dimensional structure of the binuclear metal center of phosphotriesterase. Biochemistry, 1995, 34: 7973-8.
[5] Elias M, Dupuy J, Merone L, Mandrich L, Porzio E, Moniot S, Rochu D, Lecomte C, Rossi M, Masson P, Manco G, Chabriere E. Structural basis for natural lactonase and promiscuous phosphotriesterase activities. J. Mol. Biol. 2008, 379: 1017-28.
[6] Aloulou A., Rodriguez JA, Fernandez S, Oosterhout DV, Puccinelli D, Carrere F. Exploring the specific features of interfacial enzymology based on lipase sudies. BBA. 2006, 1761:995-1013.