摘要
分子进化是从分子水平上追溯生物演变的轨迹,重建其类缘关系。从结构的角度来探讨分子进化的问题近年来逐渐受到人们的关注。
碳酸酐酶(Carbonic Anhydrase, CA)广泛分布于自然界,是一种很古老的含锌金属酶,双向催化二氧化碳的可逆水合反应,与人类健康密切相关,具有重要的生理作用,其不同的同工酶已成为不同疾病的重要靶点。
考虑到蛋白质结构在分子进化过程中表现得比序列更为保守,因此能提供更为详细的进化信息。因此,本文首先探讨了α,β和γ三类碳酸酐酶的结构进化,其中包括进化机制、药物设计信息和分类信息等。这主要是通过对各类碳酸酐酶结构域结构进行多重结构比对,构建结构系统树;根据结构系统树,利用结构QR算法(QR factorization)构建非冗余结构数据集;利用非冗余结构数据集对蛋白质数据库进行blast搜索,从而引入序列相似性较高的同源序列;在剔除同源序列结构域以外的序列部分后,用序列QR算法来构建同源序列的非冗余数据集。以非冗余结构数据集的结构比对结果来引导同源序列的非冗余数据集的多重序列比对,从而构建非冗余结构数据集的结构系统树和非冗余同源序列数据集基于结构的系统发育树,完成各类碳酸酐酶基于结构的系统发育重建。
同样从分子进化的角度,基于分子钟假设检验探讨了细胞培养对中国红豆杉细胞18S rRNA基因的影响。最后利用分子对接技术,基于两种青光眼药物对结构进化的功能类群进行了验证。
本文结论如下:
(1)γ-CA处于一个结构同源性较低的远缘超家族;α-CA则是一个从序列到结构都很保守的超家族,具有很高的结构同源性;β-CA超家族的结构同源性位于二者之间,比α-CA的结构更分化,比γ-CA的结构保守。
(2)结构、序列和功能具有密切的进化关系,为碳酸酐酶的活性改造和药物设计提供了理论基础。蛋白质结构对其功能的保持非常重要,但在满足特定结构的前提下,一些关键残基的存在,才是蛋白质功能得以实现的重要因素。
(3)不同碳酸酐酶的结构具有独特的进化保守性和特异性结构区域,为碳酸酐酶的活性改造和药物设计提供了重要线索。
功能活性的差异在于保守区域的关键残基的变化,结构特异性区域主要在疏水结构部分。通过不同残基的取代可以改变其活性,而根据特异性结构也可以设计具有高度专一性的药物。
(4)γ-CA的进化机制可能是:在进化早期通过基因复制事件形成金属络合结构,后来受到环境的压力,发生结构趋异事件,逐渐形成质子转移结构,才具备高效的催化活性。
(5)为CsoSCA作为β-CA的一个新亚类提供了有力的证据。
(6)细胞培养能在种的水平影响保守的18S rRNA基因进化,使得HG-1和Taxus chinensis的分歧时间相差约7Ma。
The studies on the evolution of structures have been around for a long time, but only recently have significant progress been made.
Carbonic anhydrase (CA, EC 4.2.1.1) are zinc-containing enzymes catalyzing the reversible hydration of CO2. They are ubiquitous in Eukarya, Archaea and Bacteria domains. The enzyme is important to many physiological processes such as respiration, CO2 transport and photosynthesis. CAs had been used as the important target proteins for drug designs.
Protein structure is more highly conserved than sequence and it can give more detailed evolutionary information, the comparative analysis of structures allows the investigation of evolutionary events. So, this dissertation studied the molecular evolution ofα-,β-, andγ-class carbonic anhydrases based on their domain structures.
To obtain a reliable analysis, we defined a subset that contains all specificities and organisms as the nonredundant structure set using QR factorization based on the multiple structural alignment of the known crystallographic structures ofα-,β-, andγ-CAs with QH and Qres as the structural homology measure. Then, we applied unweighted pair group method with arithmetic averages (UPGMA) to reconstruct structural phylogeny with 1-QH as the distance. Further analysis of the catalytic domain requires importing the sequences as well. This dissertation did so by performing a BLAST search of a carbonic anhydrase domain structure from the nonredundant structure set agaist the Swiss-Prot database one at a time. The over-represented sequences were eliminated. Using ClustalW to align the sequences and use MultiSeq to keep only the portions of the sequences that aligned to the catalytic domain in the structures. The sequence QR factorization was used to select the nonredundant sequence set. Finally, the structural alignment of the nonredundant structure set was used to guide the sequence alignment of the noredundant sequence set. The phylogenetic trees were reconstructed using neighbor-joining method with poisson distances as the metic.
Then, this dissertation discussed the effect of cell culture on the Taxus chinensis cells 18S rRNA gene based on the phylogenetic analysis and molecular clock hypothsis. At last, we validated the functional group from evolution of structures via virtual screening based on molecular docking.
The results suggest as follow:
1.α-CAs are from a superfamily with highly structural homology, with QH > 0.4 and Sc > 5.5. Only the core structure of active site ofβ-CAs is highly conserved, and theγ-CA belongs to a very diverse superfamily of proteins that share the left-handedβ-helix (LβH).
2. The protein moleculars with different sequences either can be in possession of the similar structures with the same function, or can bear different functions with some semblable structures. It is worth to note that the key residues in sequence have more important influence on protein function than structure. The relationships among sequence, structure and function provide theoretical principle for applied research of CA, such as the alteration of CA activity, and the drug design etc.
3. The substitution of resides in active site can change the activity of CA, and the specificity of active site can help for the specific-drug design. The conserved and specific regions of active site give highlight to the applied research of CAs, such as the alteration of CA activity, and the drug design etc.
4. The domain ofγ-CA underwent a process ofα-helical content from amino- terminal end to carboxyl-terminal end of the left-handedβ-helix; the capacity ofγ-CA to bind Zn occurred early in evolution and only later included the ability to catalyze the reversible hydration of CO2 efficiently for the occurrence of two loops involving Glu 62 and Glu 84 respectively and a long helix at the carboxyl-terminal end of the LβH.
5. The structural similarities are sufficient to allow recognition of CsoSCA as a member of theβ-class of carbonic anhydrase. More than that, the structural analysis strongly surpports for the CsoSCA should qualifiy as a distinct subclass ofβ-CAs.
6. Cell cultures make the evolution of Taxus chinensis cells 18S rRNA gene faster, and the divergence time between HG-1 and T. chinensis is about 7Ma.
引文
[1] Lipscomb WN, Strater N.(1996). Recent advances in zinc enzymology[J]. Chem Rev 96:2375-2434.
[2] Supuran CT, Scozzafava A, Casini A.(2003). Carbonic anhydrase inhibitors[J]. Medicinal Research Reviews 23:146-189.
[3] Hewett-Emmett D.(2000). Evolution and distribution of the carbonic anhydrase gene families[J]. EXS. 90:29-76.
[4] Supuran CT, Scozzafava A.(2002). Applications of carbonic anhydrase inhibitors and activators in therapy[J]. Expert Opinion on Therapeutic Patents 12:217-242.
[5] Meldrum NN, Roughton FJW.(1933). Carbonic anhydrase: its preparation and propeties[J]. Nature 80:113-142.
[6] Stadie WC, O'Brien H.(1933). The catalysis of the hydration of carbon dioxide and dehydration of carbonic acid by the enzyme from red blood cells[J]. J. Biochem. 103:521-529.
[7] Keilin D, Mann T.(1939). Carbonic anhydrase[J]. Nature 144:442-443.
[8] Keilin D, Mann T.(1940). Carbonic anhydrase. Purification and nature of the enzyme[J]. Biochem. J. 34:1163-1176.
[9] Keilin D, Mann T.(1944). Activity of purified carbonic anhydrase[J]. Nature 153:107-108.
[10] Bradfield JRG.(1947). Plant carbonic anhydrase[J]. Nature 159:467-468.
[11] Neish AC.(1939). Studies on chloroplasts. Their chemical composition and the distribution of certain metabolites between the chloroplasts and the remainder of the leaf[J]. Biochem. J. 33:300-308.
[12] Veitch FP, Blankenship LC.(1963). Carbonic anhydrase activity in bacteria[J]. Nature 197:76-77.
[13] Brundell J, Falkbring SO, Nyman PO.(1972). Carbonic anhydrase from Neisseria sicca strain 6021 II. Properties of the purified enzyme[J]. Biochim. Biophys. Acta 284:311-323.
[14] Adler L, Brundell J, Falkbring SO, et al.(1972). Carbonic anhydrase from Neisseria sicca strain 6021 I. Bacterial growth and purification of the enzyme[J]. Biochim. Biophys. Acta 284:298-310.
[15] Karrasch M, Bott M, Thauer RK.(1989). Carbonic anhydrase activity in acetate grown Methanosarcina barkeri[J]. Arch. Microbiol. 151:137-142.
[16] Alber BE, Ferry JG.(1994). A carbonic anhydrase from the archaeon Methanosarcina thermophila[J]. Proc. Natl. Acad. Sci. 91:6909-6913.
[17] Smith KS, Jakubzick C, Whittam TS, et al.(1999). Carbonic anhydrase is anancient enzyme widespread in prokaryotes[J]. Proc. Natl. Acad. Sci. 96:15184~15189.
[18] Thoms S.(2002). Hydrogen bonds and the catalytic mechanism of human carbonic anhydraseⅡ[ J]. J Theor Biol 215:399-404.
[19]曾广智,黄火强,谭宁华, et al.(2006).碳酸酐酶Ⅱ及其抑制剂研究进展[J].云南植物研究28:543-552.
[20] Lindskog S.(1997). Structure and mechanism of carbonic anhydrase[J]. Pharmacol Ther 74:1-20.
[21] Hewett-Emmett D, Tashian RE.(1996). Functional diversity, conservation and convergence in the evolution of theα-,β- andγ-carbonic anhydrase gene families[J]. Mol. Phylogenet. Evol. 5:50-77.
[22] Tripp BC, Smith K, Ferry JG.(2001). Carbonic anhydrase: new insights for an ancient enzyme[J]. The Journal Of Biological Chemistry 276:48615~48618.
[23] So AK, Espie GS, Williams EB, et al.(2004). A Novel Evolutionary lineage of carbonic anhydrase (ε-Class) is a component of the carboxysome shell[J]. Journal Of Bacteriology 186:623-630.
[24] Roberts SB, Lane TW, Morel FMM.(1997). Carbonic anhydrase in the marine diatom Thalassiosira weissflogi(Bacillariophyceae)[J]. J Phycol 33:845-850.
[25] Cox EH, McLendon GL, Morel FM, et al.(2000). The Active Site Structure of Thalassiosira weissflogii Carbonic Anhydrase 1[J]. Biochemistry 39:12128-12130.
[26] Mori K, Ogawa Y, Ebihara K, et al.(1999). Isolation and Characterization of CA XIV, a Novel Membrane-bound Carbonic Anhydrase from Mouse Kidney[J]. J. Biol. Chem. 274:15701-15705.
[27] Fukuzawa H, Fujiwara S, Yamamoto Y, et al.(1990). cDNA Cloning, Sequence, and Expression of Carbonic Anhydrase in Chlamydomonas reinhardtii: Regulation by Environmental CO2 Concentration[J]. Proc. Natl. Acad. Sci. 87:4383-4387.
[28] Fukuzawa H, Fujiwara S, Tachiki A, et al.(1990). Nucleotide sequences of two genes CAH1 and CAH2 which encode carbonic anhydrase polypeptides in Chlamydomonas reinhardtii[J]. Nucleic Acids Res 18:6441-6442.
[29] Chirica LC, Elleby B, Jonsson BH, et al.(1997). The Complete Sequence, Expression in Escherichia Coli, Purification and Some Properties of Carbonic Anhydrase from Neisseria Gonorrhoeae[J]. European Journal of Biochemistry 244:755-760.
[30] Guilloton MB, Korte JJ, Lamblin AF, et al.(1992). Carbonic anhydrase in Escherichia coli. A product of the cyn operon[J]. J. Biol. Chem. 267:3731-3734.
[31] Alber BE, Ferry JG.(1996). Characterization of heterologously produced carbonic anhydrase from Methanosarcina thermophila[J]. J. Bacteriol. 178:3270-3274.
[32] Smith KS, Ferry JG.(2000). Prokaryotic carbonic anhydrases[J]. FEMS Microbiology Reviews 24:335-366.
[33] Smith KS, Cosper NJ, Stalhandske C, et al.(2000). Structural and kineticcharacterization of an archaealβ-class carbonic anhydrase[J]. Journal of Bacteriology 182:6605-6613.
[34] Martin W, Muller M.(1998). The hydrogen hypothesis for the first eukaryote[J]. Nature 392:37-41.
[35] Moreira D, Lopez-Garcia P.(1998). Symbiosis between methanogenic archaea and N-proteobacteria as the origin of eukaryotes: the syntropic hypothesis[J]. J. Mol. Evol. 47:517-530.
[36] Liljas A, Laurberg M.(2000). A wheel invented three times. The molecular structures of the three carbonic anhydrases[J]. EMBO Rep 1:16-17.
[37] Silverman DN, Lindskog S.(1988). The catalytic mechanism of carbonic anhydrase: implications of a rate-limiting proteolysis of water[J]. Acc. Chem. Res. 21:30-36.
[38] Johansson IM, Forsman C.(1993). Kinetic studies of pea carbonic anhydrase[J]. Eur. J. Biochem. 218:439-446.
[39] Johansson IM, Forsman C.(1994). Solvent hydrogen isotope effects and anion inhibition of CO2 hydration catalysed by carbonic anhydrase from Pisum sativum[J]. Eur. J. Biochem. 224:901-907.
[40] Rowlett, R.S., Chance MR, Wirt MD, Sidelinger DE, et al.(1994). Kinetic and structural characterization of spinach carbonic anhydrase[J]. Biochemistry 33:13967-13976.
[41] Alber BE, Colangelo CM, Dong J, et al.(1999). Kinetic and Spectroscopic Characterization of the Gamma-Carbonic Anhydrase from the Methanoarchaeon Methanosarcina thermophila[J]. Biochemistry 38:13119-13128.
[42] Supuran CT, Scozzafava A.(2002). Applications of carbonic anhydrase inhibitors and activators in therapy[J]. Exp Opin Ther Patents 12:217-242.
[43] Supuran CT, Scozzafava A.(2000). Carbonic anhydrase inhibitors and their therapeutic potential[J]. Exp Opin Ther Patents 10:575-600.
[44] Kim G, Selengut J, Levine RL.(2000). Carbonic anhydrase III: The phosphatase activity is extrinsic[J]. Arch Biochem Biophys 377:334-340.
[45] Briganti F, Mangani S, Orioli P, et al.(1997). Carbonic anhydrase activators: X-ray crystallographic and spectroscopic investigations for the interaction of isozymes I and II with histamine[J]. Biochemistry 36:10384-10392.
[46] Loferer MJ, Tautermann CS, Loeffler HH, et al.(2003). Influence of backbone conformations of human carbonic anhydraseⅡon carbon dioxide hydration : Hydration pathways and binding of bicarbonate[J]. Am Chem Soc 125:8921-8927.
[47] Hunt JA, Ahmed M, Fierke CA.(1999). Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues[J]. Biochemistry 38:9054-9062.
[48] Jonsson BM, Hakansson K, Liljas A.(1993). The structure of human carbonic anhydraseⅡin complex with bromide and azide[J]. FEBS 322:186-190.
[49] Christianson DW, Fierke CA.(1996). Carbonic anhydrase: Evolution of the zinc binding site by nature and by design[J]. Acc Chem Res 29:331-339.
[50] Lindahl M, Svensson LA, Liljas A.(1993). Metal poison inhibition of carbonic anhydrase[J]. Protein Struct. Funct. Genet. 15:177-182.
[51] Eriksson AE, Kylsten PM, Jones TA, et al.(1988). Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: a pentacoordinated binding of the SCNG ion to the zinc at high pH[J]. Protein Struct. Funct. Genet. 4:283-293.
[52] Hakansson K, Carlsson M, Svensson LA, et al.(1992). The structure of native and apo carbonic anhydrase-II and some of its anion-ligand complexes[J]. J. Mol. Biol. 227:1192-1204.
[53] Christianson DW.(1996). Structural aspects of divergent proton translocation trajectories in carbonic anhydrasesⅡa ndⅤ[ J]. Rigaku J 13:8-15.
[54] An H, Tu C, Duda D, et al.(2002). Chemical rescue in catalysis by human carbonic anhydrasesⅡandⅢ[ J]. Biochemistry 41:3235-3242.
[55] Elder I, Han S, Tu C, et al.(2004). Activation of carbonic anhydraseⅡby active-site incorporation of histidine analogs[J]. Arc Bioch Biophys 421:283-289.
[56] Nakata K, Shimomura N, Shiina N, et al.(2002). Kinetic study of catalytic CO2 hydration by water-soluble model compound of carbonic anhydrase and anion inhibition effect on CO2 hydration[J]. J Inorg Biochem 89:255-266.
[57] Duda D, Tu C, Qian M, et al.(2001). Structural and kinetic analysis of the chemical rescue of the proton transfer function of carbonic anhydraseⅡ[J]. Biochemistry 40:1741-1748.
[58] Martensson LG, Jonsson BH, Andersson M, et al.(1992). Role of an evolutionarily invariant serine for the stability of human carbonic anhydrase II[J]. Biochim Biophys Acta 1118:179-186.
[59] Krebs JF, Fierke CA.(1993). Determinants of catalytic activity and stability of carbonic anhydrase II as revealed by random mutagenesis[J]. J. Biol. Chem. 168:948-954.
[60] Martensson LG, Jonasson P, Freskgard PO, et al.(1995). Contribution of individual tryptophan residues to the fluorescence spectrum of native and denatured forms of human carbonic anhydrase II[J]. Biochemistry 34:1011-1021.
[61] Wagner LE, Venta PJ, Tashian RE.(1991). A human carbonic anhydrase I deficiency appears to be caused by a destabilizing amino acid substitution (246- Arg His)[J]. Isozyme Bull 24:35.
[62] Tashian RE.(1992). Genetics of the mammalian carbonic anhydrases[J]. Advances in Genetics 30:321-356.
[63] Roth DE, Venta PJ, Tashian, R.E. Sly WS.(1992). Molecular Basis of Human Carbonic Anhydrase II Deficiency[J]. Proc. Natl. Acad. Sci. 89:1804-1808.
[64] Forsman C, Behravan G, Jonsson BH, et al.(1988). Histidine 64 is not required for high CO2 hydration activity of human carbonic anhydrase II[J]. FEBS Lett229:360-362.
[65] Tu CK, Silverman DN, Forsman C, et al.(1989). Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant[J]. Biochemistry 28:7913-7918.
[66] Engstrand C, Forsman C, Liang Z, et al.(1992). Proton transfer roles of lysine 64 and glutamic acid 64 replacing histidine 64 in the active site of human carbonic anhydrase II[J]. Biochim. Biophys. Acta 1122:321-326.
[67] Mitsuhashi S, Mizushima T, Yamashita E, et al.(2000). X-ray Structure ofβ-Carbonic Anhydrase from the Red Alga, Porphyridium purpureum, Reveals a Novel Catalytic Site for CO2 Hydration[J]. J. Biol. Chem. 275:5521-5526.
[68] Kimber MS, Pai EF.(2000). The active site architecture of Pisum sativumβ-carbonic anhydrase is a mirror image of that ofα-carbonic anhydrases[J]. EMBO J. 19:1407-1418.
[69] Strop P, Smith KS, Iverson TM, et al.(2001). Crystal Structure of the“cab”-typeβ-Class Carbonic Anhydrase from the Archaeon Methanobacterium thermoautotrophicum[J]. J. Biol. Chem. 276:10299-10305.
[70] Cronk JD, Endrizzi JA, Cronk MR, et al.(2001). Crystal structure of E. coliβ–carbonic anhydrase, an enzyme with an unusual pH–dependent activity[J]. Protein Science 10:911-922.
[71] Covarrubias AS, Larsson AM, Hogbom M, et al.(2005). Structure and Function of Carbonic Anhydrases from Mycobacterium tuberculosis[J]. J. Biol. Chem. 280:18782-18789.
[72] Covarrubias AS, Bergfors T, Jones TA, et al.(2006). Structural Mechanics of the pH-dependent Activity ofβ-Carbonic Anhydrase from Mycobacterium tuberculosis[J]. J. Biol. Chem. 281:4993-4999.
[73] Bjorkbacka H, Johansson IM, Forsman C.(1999). Possible roles for His 208 in the active-site region of chloroplast carbonic anhydrase from Pisum ativum[J]. Arch. Biochem. Biophys. 361:17-24.
[74] Jiang W, Gupta D.(1999). Structure of the carbonic anhydrase VI (CA6) gene: evidence for two distinct groups within theα-CA gene family[J]. Biochem. J. 344:385-390.
[75] Kisker C, Schindelin H, Alber B, et al.(1996). A left-handedβ-helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila[J]. EMBO J. 15:2323-2330.
[76] Iverson TM, Alber BE, Kisker C, et al.(2000). A closer look at the active site ofγ-carbonic anhydrases: high resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila[J]. Biochemistry 39:9222-9231.
[77] Merz KM.(1990). Insights into the function of the zinc hydroxide-Thr199-Glu106 hydrogen bonding network in carbonic anhydrases[J]. J. Mol. Biol. 214:799-802.
[78] Krebs JF, Ippolito JA, Christianson DW, et al.(1993). Structural and functionalimportance of a conserved hydrogen-bond network in human carbonic anhydrase II[J]. J. Biol. Chem. 268:27458-27466.
[79] Liang ZW, Xue YF, Behravan G, et al.(1993). Importance of the conserved active-site residues Tyr7, Glu106 and Thr199 for the catalytic function of human carbonic anhydrase II[J]. Eur. J. Biochem. 211:821-827.
[80] Tripp BC, Ferry JG.(2000). A structure-function study of a proton transport pathway in the gamma class carbonic anhydrase from Methanosarcina thermophila[J]. Biochemistry 39:9232-9240.
[81] Zimmerman SA, Ferry JG.(2006). Proposal for a Hydrogen Bond Network in the Active Site of the Prototypicγ-Class Carbonic Anhydrase[J]. Biochemistry 45:5149-5157.
[82] Henkin RI, Martin BM, Agarwal RP.(1999). Decreased parotid sailva gustin/carbonic anhydrase VI secretion: an enzyme disorder manifested by gustatory and olfactory dysfunction[J]. Am J Med Sci 318:380-391.
[83] Kivela J, Parkkila S, Parkkila AK, et al.(1999). A low concentration of carbonic anhydrase isoenzyme VI in whole saliva is associated with caries prevalence[J]. Caries Res 33:178-184.
[84] Winum J, Scozzafava A, Montero J, et al.(2006). New Zinc Binding Motifs in the Design of Selective Carbonic Anhydrase Inhibitors[J]. Mini Reviews in Medicinal Chemistry 6:921-936.
[85] Ling B, Bergenhem NCH, Dodgson SJ, et al.(1994). Determination of mRNA levels for six carbonic anhydrase isozymes in rat lung[J]. Isozyme Bull 27:47.
[86] Vullo D, Voipio J, Innocenti A, et al.(2005). Carbonic anhydrase inhibitors. Inhibition of the human cytosolic isozyme VII with aromatic and heterocyclic sulfonamides[J]. Bioorg Med Chem Lett 15:971-976.
[87] Clare BW, Supuran CT.(2006). A perspective on quantitative structure-activity relationships and carbonic anhydrase inhibitors[J]. Expert Opinion on Drug Metabolism and Toxicology 2:113-137.
[88] Pastorekova S, Parkkila S, Pastorek J, et al.(2004). Carbonic anhydrases: current state of the art, therapeutic applications and future prospects[J]. J Enzyme Inhib Med Chem 19:199-299.
[89] Supuran CT, Scozzafava A.(2000). Carbonic anhydrase inhibitors: aromatic sulfonamides and disulfonamides act as efficient tumor growth inhibitors[J]. J Enzyme Inhib 15:597-610.
[90] Dorai T, Sawczuk IS, Pastorek J, et al.(2005). The role of carbonic anhydrase IX overexpression in kidney cancer[J]. Eur J Cancer 41:2935-2947.
[91] PastorekováS, ZávadaJ.(2004). Carbonic anhydrase IX (CA IX) as a potential target for cancer therapy[J]. Cancer Therapy 2:245-262.
[92] Scozzafava A, Mastrolorenzo A, Supuran CT.(2004). Modulation of carbonic anhydrase activity and its applications in therapy[J]. Expert Opinion onTherapeutic Patents 14:667-702.
[93] Thiry A, DognéJM, Masereel B, et al.(2006). Targeting tumor-associated carbonic anhydrase IX in cancer therapy[J]. Trends in Pharmacological Sciences 27:566-573.
[94] Nishimori I, Minakuchi T, Kohsaki T, et al.(2007). Carbonic anhydrase inhibitors: Theβ-carbonic anhydrase from Helicobacter pylori is a new target for sulfonamide and sulfamate inhibitors[J]. Bioorganic & Medicinal Chemistry Letters 17:3585-3594.
[95] Nishimori I, Minakuchi T, Morimoto K, et al.(2006). Carbonic Anhydrase Inhibitors: DNA Cloning and Inhibition Studies of theα-Carbonic Anhydrase from Helicobacter pylori, A New Target for Developing Sulfonamide and Sulfamate Gastric Drugs[J]. J. Med. Chem. 49:2117-2126.
[96] Nishimori I, Vullo D, Innocenti A, et al.(2005). Carbonic Anhydrase Inhibitors. The Mitochondrial Isozyme VB as a New Target for Sulfonamide and Sulfamate Inhibitors[J]. J. Med. Chem. 48:7860-7866.
[97] Sun MK, ADL.(2002). Carbonic anhydrase gating of attention: memory therapy and enhancement[J]. Trends in Pharmacological Sciences 23:83-89.
[98] Liu Z, He D.(1998). Special speleothems in cenment-grouting tunels and their implications of the atmospheric CO2 sink[J]. Environmental Geology 5:258-262.
[99]刘再华.(2001).碳酸酐酶对碳酸盐溶解的催化作用及其在大气CO2沉降中的意义[J].地质学报75:432-432.
[100] Gillon J, Yaki D.(2001). Influence of carbonic anhydrase activity in terrestrial vegetation on the 18O content of atmospheric CO2[J]. Science 291:2584-2587.
[101] Liu ZH.(2001). The role of carbonic anhydrase as an activator in carbonate rock dissolution : implication of more atmospheric CO2 sink[J]. Acta Geologica Sinica 75:275-278.
[102] Li W, Yu LJ, Yuan DX, et al.(2004). Bacteria biomass and carbonic anhydrase activity in some karst areas of Sout hwest China[J]. Journal of Asian Earth Sciences 24:145-152.
[103] Li W, Yu LJ, He QF, et al.(2005). Effects of microbes and their carbonic anhydrase on Ca2+ and Mg2+ migration in column-built leached soil-limestone karst systems[J]. Applied Soil Ecology 29:274-281.
[104]李涛,余龙江.(2006).西南岩溶环境中典型植物适应机制的初步研究[J].地学前缘(中国地质大学(北京) ;北京大学) 13:180-184.
[105] Parisi G, Fornasari M, Echave J.(2000). Evolutionary Analysis ofγ-Carbonic Anhydrase and Structurally Related Proteins[J]. Molecular Phylogenetics and Evolution 14:323-334.
[106] Lane TW, Morel FMM.(2000). Regulation of carbonic anhydrase expression by zinc, cobalt, and carbon dioxide in the marine diatom Thalassiosira weissflogii[J]. Plant Physiol 123:345-352.
[107] Sawaya MR, Cannon GC, Heinhorst S, et al.(2006). The Structure ofβ-Carbonic Anhydrase from the Carboxysomal Shell Reveals a Distinct Subclass with One Active Site for the Price of Two[J]. J. Biol. Chem. 281:7546-7555.
[108] Hirasuna TJ, Pestchanker LJ, Srinivasan C.(1996). Taxol production in suspension cultures of Taxus baccata[J]. Plant Cell Tissue Organ Cult. 44:95-102.
[109] Zhong JJ.(2002). Plant cell culture for production of paclitaxel and other taxanes[J]. Journal of Bioscience and Bioengineering 94:591-599.
[110] Baebler S, Hren M, Camloh M, et al.(2005). Establishment of cell suspension cultures of yew (Taxus×media rehd.) and assessment of their genomic stability[J]. In Vitro Cellular and Developmental Biology - Plant 41:338-343.
[111] Yu LJ, Zhang CH, Mei XG, et al.(1998). Somaclonal variation in the number of chromosome and the number of nuclei in cultured Taxus chinensis cells[J]. J. Huazhong University of Science and Technology Sin. 26:100-102.
[112] Woese CR, Olsen GJ, Ibba M, et al.(2000). Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process[J]. Microbiol Mol Biol Rev 64:202-236.
[113] Socolich M, Lockless SW, Russ WP, et al.(2005). Evolutionary information for specifying a protein fold[J]. Nature 437:512-518.
[114] Castresana J.(2000). Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis[J]. Molecular Biology and Evolution 17:540-552.
[115] Doolittle WF.(1999). Phylogenetic classification and the universal tree[J]. Science 284:2124-2128.
[116] Doolittle RF.(1986) Of URFs and ORFs: A primer on how to analyze derived amino acid sequences. California: University Science Books, Mill Valley.
[117]罗静初等译.(2002)生物信息学概论.北京:北京大学出版社.
[118]胡胜明,王钰,贺福初, et al.(2000).蛋白质超家族分子进化研究的一种新方法[J].科学通报45:2310-2315.
[119]张成岗,贺福初.(2002)生物信息学方法与实践.北京:科学出版社.
[120]黄京飞,刘次全.(1997).从氨基酸残基的静态可及性探讨组蛋白的分子进化[J].动物学研究18:429-435.
[121] Krissinel E, Henrick K.(2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions[J]. Acta Cryst D60:2256-2268.
[122] Berman HM, Westbrook J, Feng Z, et al.(2000). The Protein Data Bank[J]. Nucleic Acids Research 28:235-242.
[123] Gibrat JF, Madej T, Bryant SH.(1996). Surprising similarities in structure comparison[J]. Curr Opin Struct Biol 6:377-385.
[124] Holm L, Sander C.(1994). Searching protein structure databases has come of age[J]. Proteins 19:165-173.
[125]李衍达,孙之荣等译.(2000)生物信息学:基因和蛋白质分析的实用指南.北京:清华大学出版社.
[126] Berman HM, Henrick K, Nakamura H.(2003). Announcing the worldwide Protein Data Bank[J]. Nature Structural Biology 10:980.
[127] Smith TF, Waterman MS.(1981). Identification of common molecular subsequences[J]. J. Mol. Biol. 147:195-197.
[128] Chothia C.(1992). One thousand families for the molecular biologist[J]. Nature 357:543-544.
[129] Chothia C, Lesk AM.(1986). The relation between the divergence of sequence and structure in proteins[J]. EMBO J. 5:823-826.
[130] Murzin AG.(1998). How far divergent evolution goes in proteins[J]. Curr Opin Struct Biol 8:380-387.
[131] Russell RB, Barton GJ.(1992). Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels[J]. Proteins: Struct. Funct. Genet. 14:309-323.
[132] Humphrey W, Dalke A, Schulten K.(1996). VMD-Visual Molecular Dynamics[J]. J. Molec. Graphics 14:33-38.
[133] Roberts E, Eargle J, Wright D, et al.(2006). MultiSeq: unifying sequence and structure data for evolutionary analysis[J]. BMC Bioinformatics 7:382.
[134] Guex N, Diemand A, Peitsch MC.(1999). Protein modelling for all[J]. Trends Biochem Sci. 24:364-367.
[135] Canutescu AA, Dunbrack RLJ.(2005). MollDE: a homology modeling framework you can click with[J]. Bioinformatics 21:2914-2916.
[136] Canutescu AA, Shelenkov AA, Dunbrack RLJ.(2003). A graph-theory algorithm for rapid protein side-chain prediction[J]. Protein Sci. 12:2001-2014.
[137] Neshich G, Borro LC, Higa RH, et al.(2005). The Diamond STING server[J]. Nucleic Acids Res. 33:29-35.
[138] Marti-Renom MA, Stuart AC, Fiser A, et al.(2000). Comparative protein structure modeling of genes and genomes[J]. Annu Rev Biophys Biomol Struct 29:291-325.
[139] Pettersen EF, Goddard TD, Huang CC, et al.(2004). UCSF Chimera-a visualization system for exploratory research and analysis[J]. J Comput Chem 25:1605-1612.
[140] Abyzov A, Errami M, Leslin CM, et al.(2005). Friend, an integrated analytical front-end application for bioinformatics[J]. Bioinformatics 21:3677-3678.
[141] Wang Y, Geer LY, Chappey C, et al.(2000). Cn3D: sequence and structure views for Entrez[J]. Trends Biochem Sci 25:300-302.
[142] Attwood TK, Miller CJ.(2001). Which craft is best in bioinformatics?[J]. Comput Chem 25:329-339.
[143] O`Donoghue P, Luthey-Schulten Z.(2005). Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy ofInformation[J]. J. Mol. Biol. 346:875-894.
[144] Sethi A, O`Donoghue P, Luthey-Schulten Z.(2005). Evolutionary profiles from the QR factorization of multiple sequence alignments[J]. Proc Natl Acad Sci USA 102:4045-4050.
[145] O`Donoghue P, Sethi A, Woese CR, et al.(2005). The evolutionary history of Cys-tRNACys formation[J]. Proc Natl Acad Sci 102:19003-19008.
[146] Sethi A, Eargle J, O`Donoghue P, et al.(2004). Evolutionary profiles derived from QR factorization of multiple sequence and structural alignments[J]. CASP6 Abstracts :134-135.
[147] Eidhammer I, Jonassen I, Taylor WR.(2000). Structure comparison and structure patterns[J]. J Comput Biol 7:685-716.
[148] Zhu J, Weng Z.(2005). FAST: A Novel Protein Structure Alignment Algorithm[J]. Proteins: Structure, Function and Bioinformatics 14:417-423.
[149] Russell RB.(2006) STAMP Structural Alignment of Multiple Proteins Version 4.3 User Guide.
[150] Argos P, Rossmann M.(1976). Exploring structural homology of proteins[J]. J. Mol. Biol. 105:75-95.
[151] Barton GJ.(1993). An efficient algorithm to locate all locally optimal alignments[J]. Comp. App. Biosci. 9:729-734.
[152] Eastwood MP, Hardin C, Luthey-Schulten Z, et al.(2001). Evaluating protein structure prediction schemes using energy landscape theory[J]. IBM. J. Res. Dev. 45:475-497.
[153] O`Donoghue P, Luthey-Schulten Z.(2003). On the Evolution of Structure in Aminoacyl-tRNA Synthetases[J]. Microbiology And Molecular Biology Reviews 67:550-573.
[154] Zuckerkandl E, Pauling L.(1965). Molecules as documents of evolutionary history[J]. J. Theor. Biol. 8:357-366.
[155] DeLong EF, Pace NR.(2001). Environmental diversity of bacteria and archaea[J]. Syst. Biol. 50:470-478.
[156] Woese CR, Fox GE.(1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms[J]. Proc. Natl Acad. Sci. 74:5088-5090.
[157] Darwin C.(1887). The Life and Letters of Charles Darwin, Including an Autobiographical Chapter, John Murray, London[J].
[158] Feng DF, Doolittle RF.(1987). Progressive sequence alignment as a prerequisite to correct phylogenetic trees[J]. J. Mol. Evol. 25:351-360.
[159] Bateman A, Coin L, Durbin R, et al.(2004). The Pfam protein families database[J]. Nucl. Acids Res. 32:D138-D141.
[160] Pandit SB, Bhadra R, Gowri VS, et al.(2004). Supfam: a database of sequence superfamilies of protein domains[J]. BMC Bioinformat. 5:28.
[161] Stebbings LA, Mizuguchi K.(2004). HOMSTRAD: recent developments in thehomologous protein structure alignment database[J]. Nucl. Acids Res. 32:D203-D207.
[162] Gribskov M, McLachlan M, Eisenberg D.(1987). Profile analysis: detection of distantly related proteins[J]. Proc. Natl Acad. Sci. 84:4355-4358.
[163] Sonnhammer ELL, Eddy SR, Durbin R.(1997). Pfam: a comprehensive database of protein domain families based on seed alignments[J]. Proteins: Struct. Funct. Genet. 28:405-420.
[164] Lupas AN, Ponting CP, Russell RB.(2001). On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?[J]. J. Struct. Biol. 134:191-203.
[165] Sadreyev R, Grishin N.(2003). COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance[J]. J. Mol. Biol. 326:317-336.
[166] Tang CL, Xie L, Koh IYY, et al.(2003). On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles[J]. J. Mol. Biol. 334:1043-1062.
[167] O`Sullivan O, Suhre K, Abergel C, et al.(2004). 3DCoffee: combining protein sequences and structures within multiple sequence alignments[J]. J. Mol. Biol. 340:385-395.
[168] Tramontano A, Morea V.(2003). Assessment of homology-based predictions in CASP5[J]. Proteins: Struct. Funct. Genet. 53:352-368.
[169] Petrey D, Xiang Z, Tang CL, et al.(2003). Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling[J]. Proteins: Struct. Funct. Genet. 53:430-435.
[170] Bickel PJ, Kechris KJ, Spector PC, et al.(2002). Finding important sites in protein sequences[J]. Proc. Natl Acad. Sci. 99:14764-14771.
[171] Shakhnovich BE, Dokholyan NV, DeLisi C, et al.(2003). Functional fingerprints of folds: evidence for correlated structure-function evolution[J]. J. Mol. Biol. 326:1-9.
[172] Hardin C, Pogorelov TV, Luthey-Schulten Z.(2002). Ab initio protein structure prediction[J]. Curr. Opin. Struct. Biol. 12:176-181.
[173] Russ WP, Ranganathan R.(2002). Knowledgebased potential functions in protein design[J]. Curr. Opin. Struct. Biol. 12:447-452.
[174] Amann RI, Ludwig W, Schleifer KH.(1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J]. Microbiol. Rev. 59:143-169.
[175] Pace NR.(1997). A molecular view of microbial diversity and the biosphere[J]. Science 276:734-740.
[176] Tyson GW, Chapman J, Hugenholtz P, et al.(2004). Community structure and metabolism through reconstruction of microbial genomes from the environment[J].Nature 428:37-43.
[177] Venter JC, Remington K, Heidelberg JF, et al.(2004). Environmental genome shotgun sequencing of the Sargasso Sea[J]. Science 304:66-74.
[178] Holm L, Sander C.(1998). Removing nearneighbour redundancy from large protein sequence collections[J]. Bioinformatics 14:423-429.
[179] O`Donovan C, Martin MJ, Glemet E, et al.(1999). Removing redundancy in SWISS-PROT and TrEMBL[J]. Bioinformatics 15:258-259.
[180] Wang G, Dunbrack RL, Jr.(2003). PISCES: a protein sequence culling server[J]. Bioinformatics 19:1589-1591.
[181] Park J, Holm L, Heger A, et al.(2000). RSDB: representative protein sequence databases have high information content[J]. Bioinformatics 16:458-464.
[182] May ACW.(2001). Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics[J]. Protein Eng. 14:209-217.
[183] Rogen P, Bohr H.(2003). A new family of global protein shape descriptors[J]. Math. Biosci. 182:167-181.
[184] Olkin JA, Heck LP, Naghshineh K. Automated placement of transducers for active noise control: performance measures. In IEEE Proceedings of International Conference on Acoustics, Speech, and Signal Processing. Atlanta, 1996:969-972.
[185] Heck LP, Olkin JA, Naghshineh K.(1998). Transducer placement for broadband active vibration control using a novel multidimensional qr factorization[J]. J. Vib. Acoust. 120:663-670.
[186] Sokal RR, Michener CD.(1958). A statistical method for evaluating systematic relationships[J]. Univ. Kansas Sci. Bull. 28:1409-1438.
[187] Felsenstein J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach[J]. J Mol Evol 17:368-376.
[188] Hollich V, Milchert L, Arvestad L, et al.(2005). Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction[J]. Mol Biol Evol 22:2257-2264.
[189] Zuckerkandl E, Pauling L.(1965) Evolutionary divergence and convergence in proteins. NewYork: Academic Press.
[190] MARK P.(1999). Inferring the historical patterns of biological evolution[J]. Nature 401:877-884.
[191] Sarich VM, Wilson AC.(1967). Rates of albumin evolution in primates[J]. Anthropology 58:142-148.
[192] Li P, Bousquet J.(1992). Relative-Rate Test for Nucleotide Substitutions between Two Lineages[J]. Mol Biol Evol 9:1185-1187.
[193] Tajima F.(1993). Simple Methods for Testing the Molecular Evolutionary Clock Hypothesis[J]. Genetics 135:599-607.
[194] Murzin AG, Brenner SE, Hubbard T, et al.(1995). SCOP: a structural classificationof proteins database for the investigation of sequences and structures[J]. J. Mol. Biol. 247:536-540.
[195] Vaara M.(1992). Eight bacterial proteins, including UDP-N-acetylglucosamine acyltransferase (LpxA) and three other transferases of Escherichia coli, consist of a six-residue periodicity theme[J]. FEMS Microbiol. Lett. 97:249-254.
[196] Vuorio R, Harkonen T, Tolvanen M, et al.(1994). The novel hexapeptide motif found in the acetyltransferases LpxA and LpxD of lipid A biosynthesis is conserved in various bacteria[J]. FEBS Lett. 337:289-292.
[197] Benner SE, Koehl P, Levitt M.(2000). The ASTRAL compendium for structure and sequence analysis[J]. Nucleic Acids Res. 28:254-256.
[198] Doolittle RF.(1994). Convergent evolution: The need to be explicit[J]. Trends Biochem. Sci. 19:15-18.
[199] Taylor WR, Orengo CA.(1989). Protein structure alignment[J]. J. Mol. Biol. 208:208-229.
[200] Nicholas KB, Nicholas HBJ.(1997) GeneDoc: A tool for editing and annotating multiple sequence alignments.
[201] Raetz C, Roderick S.(1995). A left-handed parallelβhelix in the structure of UDP-N-acetylglucosamine acyltransferase[J]. Science 270:997-1000.
[202] Beaman TW, Blanchard JS, Roderick SL.(1998). The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase[J]. Biochemistry 17:10363-10369.
[203] Pye VE, Tingey AP, Robson RL, et al.(2004). The Structure and Mechanism of Serine Acetyltransferase from Escherichia coli[J]. The Journal Of Biological Chemistry 279:40729-40736.
[204] Krebs JF, Fierke CA, Alexander RS, et al.(1991). Conformational mobility of His-64 in the Thr-200-Ser mutant of human carbonic anhydrase II[J]. Biochemistry 30:9153-9160.
[205] Nair SK, Christianson DW.(1991). Structural properties of human carbonic anhydrase II at pH 9.5[J]. Biochem. Biophys. Res. Commun. 181:579-584.
[206] Nair SK, Christianson DW.(1991). Unexpected pH-dependent conformation of His-64, the proton shuttle of carbonic anhydrase II[J]. J. Am. Chem. Soc. 113:9455-9458.
[207] Gan HH, Perlow RA, Roy S, et al.(2002). Analysis of protein sequence/structure similarity relationships[J]. Biophys. J. 83:2781-2791.
[208] Olsen LR, Roderick SL.(2001). Structure of the Escherichia coli GlmU Pyrophosphorylase and Acetyltransferase Active Sites[J]. Biochemistry 40:1913-1921.
[209] Olsen LR, Huang B, Vetting MW, et al.(2004). Structure of Serine Acetyltransferase in Complexes with CoA and Its Cysteine Feedback Inhibitor[J]. Biochemistry 43:6013-6019.
[210] Beaman TW, Sugantino M, Roderick SL.(1998). Structure of the Hexapeptide Xenobiotic Acetyltransferase from Pseudomonas aeruginosa[J]. Biochemistry 37:6689-6696.
[211] Wyckoff TJO, Raetz CRH.(1999). The Active Site of Escherichia coli UDP-N-acetylglucosamine Acyltransferase. Chemical modification and site-directed mutagenesis[J]. J. Biol. Chem. 274:27047-27055.
[212] Marchler-Bauer A, Anderson JB, Derbyshire MK, et al.(2007). CDD: a conserved domain database for interactive domain family analysis[J]. Nucleic Acids Res 25:D237-240.
[213] Hulo N, Bairoch A, Bulliard V, et al.(2006). The PROSITE database[J]. Nucleic Acids Res. 34:D227-D230.
[214] Sigrist CJA, Cerutti L, Hulo N, et al.(2002). PROSITE: a documented database using patterns and profiles as motif descriptors[J]. Brief Bioinform. 3:265-274.
[215] Leggat W, Dixon R, Saleh S, et al.(2005). A novel carbonic anhydrase from the giant clam Tridacna gigas contains two carbonic anhydrase domains[J]. FEBS J. 272:3297-3305.
[216] Lehtonen J, Shen B, Vihinen M, et al.(2004). Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family[J]. J Biol Chem 279:2719-2727.
[217] Fleming RE, Parkkila S, Parkkila AK, et al.(1995). Carbonic anhydrase IV expression in rat and human gastrointestinal tract regional, cellular, and subcellular localization[J]. J. Clin. Invest. 96:2907-2913.
[218] Pastorekova S, Parkkila S, Parkkila AK, et al.(1997). Carbonic anhydrase IX, MN/CA IX: analysis of stomach complementary DNA sequence and expression in human and rat alimentary tracts[J]. Gastroenterology 112:398-408.
[219] Kyllonen MS, Parkkila S, Rajaniemi H, et al.(2003). Localization of carbonic anhydrase XII to the basolateral membrane of H+-secreting cells of mouse and rat kidney[J]. J. Histochem. Cytochem. 51:1217-1224.
[220] Parkkila S, Parkkila AK, Rajaniemi H, et al.(2001). Expression of membrane-associated carbonic anhydrase XIV on neurons and axons in mouse and human brain[J]. Proc. Natl. Acad. Sci. 98:1918-1923.
[221] Leinonen J, Parkkila S, Kaunisto K, et al.(2001). Secretion of carbonic anhydrase isoenzyme VI (CA VI) from human and rat lingual serous von Ebner's glands[J]. J. Histochem. Cytochem. 49:657-662.
[222] Shah GN, Hewett-Emmett D, Grubb JH, et al.(2000). Mitochondrial carbonic anhydrase CA VB: differences in tissue distribution and pattern of evolution from those of CA VA suggest distinct physiological roles[J]. Proc. Natl. Acad. Sci. 97:1677-1682.
[223] Nishimori I. (2004) Acatalytic CAs: Carbonic anhydrase-related proteins. In Carbonic Anhydrase: Its Inhibitors and Activators ( Supuran CT, Scozzafava A,Conway J, eds.), pp. 25-43, CRC Press, Boca Raton.
[224] Kumar S, Tamura K, Nei M.(2004). MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment[J]. Briefings in Bioinformatics 5:150-163.
[225] Sly WS, Hu PY.(1995). Human carbonic anhydrases and carbonic anhydrase deficiencies[J]. Annu. Rev. Biochem. 64:375-401.
[226] Eriksson AE, Jones TA, Liljas A.(1988). Refined structure of human carbonic anhydrase II at 2.0 angstrom resolution[J]. Protein Struct. Funct. Genet. 4:274-282.
[227] Huang S, Xue Y, Sauer-Eriksson E, et al.(1998). Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae and its complex with the inhibitor acetazolamide[J]. J. Mol. Biol. 283:301-310.
[228] Eriksson AE, Liljas A.(1993). Refined structure of bovine carbonic anhydrase III at 2.0 A resolution[J]. Proteins: Struct., Funct., Genet. 16:29-42.
[229] Jewell DA, Tu CK, Paranawithana SR, et al.(1991). Enhancement of the catalytic properties of human carbonic anhydrase III by site-directed mutagenesis[J]. Biochemistry 30:1484-1490.
[230] Duda DM, Tu C, Fisher SZ, et al.(2005). Human Carbonic Anhydrase III: Structural and Kinetic Study of Catalysis and Proton Transfer[J]. Biochemistry 44:10046-10053.
[231] Elder I, Fisher Z, Laipis PJ, et al.(2007). Structural and Kinetic Analysis of Proton Shuttle Residues in the Active Site of Human Carbonic Anhydrase III[J]. PROTEINS: Structure, Function, and Bioinformatics 68:337-343.
[232] LoGrasso PV, Tu CK, Chen X, et al.(1993). Influence of amino-acid replacement at position 198 on catalytic properties of zinc-bound water in human carbonic anhydrase III[J]. Biochemistry 32:5786-5791.
[233] Ren X, Jonsson BH, Lindskog S.(1991). Some properties of site-specific mutants of human carbonic anhydrase II having active-site residues characterizing carbonic anhydrase III[J]. Eur. J. Biochem. 201:417-420.
[234] LoGrasso PV, Tu CK, Jewell DA, et al.(1991). Catalytic enhancement of human carbonic anhydrase III by replacement of phenylalanine-198 with leueine[J]. Biochemistry 30:8463-8470.
[235] Tamai S, Waheed A, Cody LB, et al.(1996). Gly-63 -> Gln substitution adjacent to His-64 in rodent carbonic anhydrase IVs largely explains their reduced activity[J]. Proc. Natl. Acad. Sci. 93:13647-13652.
[236] Huang JF, Blundell TL.(1999). The relations of protein sequence and structural conservation with function[J]. Zoological Research 20:21-25.
[237] Bergenhem N, Carlsson U.(1990). Partial amino acid sequence of erythrocyte carbonic anhydrase from tiger shark[J]. Comp. Biochem. Physiol. 95B:205-213.
[238] Hewett-Emmett D, Tashian RE. (1991) Structure and evolutionary origins of the carbonic anhydrase multigene family. In The Carbonic Anhydrases: CellularPhysiology and Molecular Genetics ( Dodgson SJ, Tashian RE, Gros G, Carter ND, eds.), pp. 15-32, Plenum Press, New York.
[239] Kim CY, Whittington DA, Chang JS.(2002). Structural aspects of isozyme selectivity in the binding of inhibitors to carbonic anhydrasesⅡandⅣ[J]. J Med Chem 45:888-893.
[240] Rousselle AV, Heymann D.(2002). Osteoclastic acidification pathways during bone resorption[J]. Bone 30:533-540.
[241] Boriack-Sjodin PA, Heck RW, Laipis PJ, et al.(1995). Structure determination of murine mitochondrial carbonic anhydrase V at 2.45-A resolution: implications for catalytic proton transfer and inhibitor design[J]. Proc. Natl. Acad. Sci. 92:10949-10953.
[242] Taniuchi K, Nishimori I, Takeuchi T, et al.(2002). Developmental expression of carbonic anhydrase-related proteins VIII, X, and XI in the human brain[J]. Neuroscience 112:93-99.
[243] Taniuchi K, Nishimori I, Takeuchi T, et al.(2002). cDNA cloning and developmental expression of murine carbonic anhydrase-related proteins VIII, X, and XI[J]. Brain Res Mol Brain Res 109:207-215.
[244] Hirota J, Ando H, Hamada K, et al.(2003). Carbonic anhydrase-related protein is a novel binding protein for inositol 1,4,5-trisphosphate receptor type 1[J]. Biochem J 372:435-441.
[245] Morimoto K, Nishimori I, Takeuchi T, et al.(2005). Overexpression of carbonic anhydrase-related protein XI promotes proliferation and invasion of gastrointestinal stromal tumors[J]. Virchows Arch 447:66-73.
[246] Bergenhem NC, Hallberg M, Wisen S.(1998). Molecular characterization of the human carbonic anhydrase-related protein (HCA-RP VIII)[J]. Biochim Biophys Acta 1384:294-298.
[247] Karhumaa P, Leinonen J, Parkkila S, et al.(2001). The identification of secreted carbonic anhydrase VI as a constitutive glycoprotein of human and rat milk[J]. Proc. Natl. Acad. Sci. 98:11604-11608.
[248] Kimoto M, Kishino M, Yura Y, et al.(2006). A role of salivary carbonic anhydrase VI in dental plaque[J]. Arch Oral Biol 51:117-122.
[249] Zavadova Z, Zavada J.(2005). Carbonic anhydrase IX (CA IX) mediates tumor cell interactions with microenvironment[J]. Oncol Rep. 13:977-982.
[250] Stams T, Nair SK, Okuyama T, et al.(1996). Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8-A resolution[J]. Proc. Natl. Acad. Sci. 93:13589-13594.
[251] Zhu X, Sly W.(1990). Carbonic anhydrase IV from human lung. Purification, characterization, and comparison with membrane carbonic anhydrase from human kidney[J]. J Biol Chem 265:8795-8801.
[252] Hilvo M, Tolvanen M, Clark A, et al.(2005). Characterization of CA XV, a newGPI-anchored form of carbonic anhydrase[J]. Biochem J 392:83-92.
[253] Barnea G, Silvennoinen O, Shaanan B, et al.(1993). Identification of a carbonic anhydrase-like domain in the extracellular region of RPTP gamma defines a new subfamily of receptor tyrosine phosphatases[J]. Mol Cell Biol 13:1497-1506.
[254] Soltes-Rak E, Mulligan ME, Coleman JR.(1997). Identification and characterization of a gene encoding a vertebrate-type carbonic anhydrase in cyanobacteria[J]. J Bacteriol 179:769-774.
[255] Carter CJ, Thornburg RW.(2004). Tobacco Nectarin III is a bifunctional enzyme with monodehydroascorbate reductase and carbonic anhydrase activities[J]. Plant Mol Biol 54:415-425.
[256] Hou WC, Liu JS, Chen HJ, et al.(1999). Dioscorin, the major tuber storage protein of yam (Dioscorea batatas decne) with carbonic anhydrase and trypsin inhibitor activities[J]. J Agric Food Chem. 47:2168-2172.
[257] Kono M, Hayashi N, Samata T.(2000). Molecular mechanism of the nacreous layer formation in Pinctada maxima[J]. Biochem Biophys Res Commun 269:213-218.
[258] Miyamoto H, Miyoshi F, Kohno J.(2005). The carbonic anhydrase domain protein nacrein is expressed in the epithelial cells of the mantle and acts as a negative regulator in calcification in the mollusc Pinctada fucata[J]. Zoolog Sci 22:311-315.
[259] Badger MR, Price GD.(1994). The role of carbonic anhydrase in photosynthesis[J]. Annu. Rev. Plant Physiol. Plant Mol. 45:369-392.
[260] Smith KS, Ferry JG.(1999). A Plant-Type (beta-Class) Carbonic Anhydrase in the Thermophilic Methanoarchaeon Methanobacterium[J]. J. Bacteriol. 181:6247-6253.
[261] [261] Bracey MH, Christiansen J, Tovar P, et al.(1994). Spinach Carbonic Anhydrase: Investigation of the Zinc-Binding Ligands by Site-Directed Mutagenesis, Elemental Analysis, and EXAFS[J]. Biochemistry 33:13126-13131.
[262] Group MSAD.(1999). Metalloprotein site database and browser (MDB). MDB, Release 1.4. http://metallo.scripps.edu/.[J].
[263] Rowlett RS, Tu C, McKay MM, et al.(2002). Kinetic characterization of wild-type and proton transfer-impaired variants ofβ-carbonic anhydrase from Arabidopsis thaliana[J]. Arch. Biochem. Biophys. 404:197-209.
[264] Holm L, Sander C.(1997). Dali/FSSP classification of three-dimensional protein folds[J]. Nucleic Acids Res. 25:231-234.
[265] Kleywegt GJ.(1999). Recognition of spatial motifs in protein structures[J]. J. Mol. Biol. 285:1887-1897.
[266] Merlin C, Masters M, McAteer S, et al.(2003). Why Is Carbonic Anhydrase Essential to Escherichia coli?[J]. J. Bacteriol. 185:6415-6424.
[267] Altschul SF, Gish W, Miller W, et al.(1990). Basic local alignment search tool[J]. J. Mol. Biol. 215:403-410.
[268] Notredame C, Higgins D, Heringa J.(2000). T-Coffee: A novel method for multiple sequence alignments[J]. J. Mol. Biol. 302:205-217.
[269] Kumar S.(1996). PHYLTEST: A PROGRAM FOR TESTING PHYLOGENETIC HYPOTHESIS. Version 2.0[J]. Pennsylvania State University .
[270] Kimura M.(1980). Simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences[J]. J. Mol. Evol. 16:111-120.
[271] Savard L, Li P, Strauss SH, et al.(1994). Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants[J]. Proc. Natl. Acad. Sci. USA 91:5263-5167.
[272] Wang XQ, Tank DC, Sang T.(2000). Phylogeny and divergence within the pine family:evidence from three genomes[J]. Mol. Biol. Evol. 17:733-781.
[273] Chaw SM, Parkinson CL, Cheng Y, et al.(2000). Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers[J]. Proc. Natl. Acad. Sci. USA 97:4086-4091.
[274] Wang XQ, Shu YQ.(2000). Chloroplast matK gene phylogeny of Taxaceae and Cephalotaxaceae, with additional reference to the systematic position of Nageia[J]. Acta Phytotaxon. Sin. 38:201-210.
[275] Wang T, Su YJ, Zheng B, et al.(2002). Cladistic analysis of sequences of chloroplast rbcL gene and trnL-trnF intergenic spacer in Taxaceae and related taxa[J]. Acta Scientiarum Naturalium Universitatis Sunyatseni Sin. 41:71-74.
[276] Fu LG.(1984). The research of Cephalotaxus[J]. Acta Phytotaxon. Sin. 22:277-288.
[277] Hart JA.(1987). A cladistic analysis of conifers: Preliminary results[J]. J. Arnold. Arbor. 68:269-307.
[278] Brunsfeld SJ, Soltis PS, Soltis DE, et al.(1994). Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae: evidence from rblL sequences[J]. Syst. Bot. 19:253-262.
[279] Stefanovic S, Jager M, Deutsch J, et al.(1998). Phylogenetic relationships of conifers inferred from partial 28S rRNA gene sequences[J]. Am. J. Bot. 85:688-697.
[280] Gadek PA, Alpers DL, Heslewood MM, et al.(2000). Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach[J]. Am. J. Bot. 87:1044-1057.
[281] Kusumi J, Tsumura Y, Yoshimaru H, et al.(2000). Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene,chlL gene,trnL-trnF IGS region,and trnL intron sequences[J]. Am. J. Bot. 87:1480-1488.
[282]马晶,胡延丽.(2001).碳酸酐酶抑制剂的研究和临床评价[J].国外医药:合成药.生化药.制剂分册22:27-28.
[283] Supuran CT, Scozzafava A.(2000). Carbonic anhydrase inhibitors and their therapeutic potential[J]. Expert Opinion on Therapeutic Patents 10:575-600.
