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研究生:郭玉梅
研究生(外文):Yu-Mei Kuo
論文名稱:利用生物資訊學來探討冰花SKD1的結構與功能
論文名稱(外文):Study on the Structure and Function of Suppressor of K+ Transport Growth Defect (SKD1) Protein from Mesembryanthemum crystallinum using Bioinformatics
指導教授:周昌弘周昌弘引用關係
指導教授(外文):Chang-Hung Chou
學位類別:碩士
校院名稱:國立中山大學
系所名稱:生物科學系研究所
學門:生命科學學門
學類:生物學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:99
中文關鍵詞:冰花鉀離子吸收缺陷性狀生物資訊學結構-功能
外文關鍵詞:Mesembryanthemum crystallinumBioinformaticsstructure-functionSuppressor of K+ Transport Growth Defect
相關次數:
  • 被引用被引用:1
  • 點閱點閱:203
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  • 下載下載:56
  • 收藏至我的研究室書目清單書目收藏:0
本研究發現冰花SKD1蛋白質除具有MIT domain及AAA-ATPase domain外,冰花SKD1蛋白質的胺基酸序列與二級結構相當於酵母菌的VPS4(END13)蛋白質,也間接預測到冰花SKD1蛋白質具有特殊的NACHT domain 特徵,再依據蛋白質-蛋白質交互作用的原理,透過酵母菌雙雜合系統的實驗數據資料庫,篩選到BRO1 (HEAT repeat) 與VPS4 (NACHT domain) 產生蛋白質間交互作用的候選者,相對地,BRO1_YEAST (HEAT repeat)與AIP1_YEAST (WD40 repeat), AIP1_YEAST (WD40 repeat)與ABP1_YEAST (ADF domain), ABP1_YEAST (ADF domain)與ARP2_YEAST (ACTIN domain)會互相交互作用,這些蛋白質在細胞裡作為細胞骨架的結構蛋白質,最有可能關聯到鉀離子吸收與耐鹽機制,此種研究方法亦可應用在其它真核生物中找尋與鉀離子運輸相關的功能蛋白質。
SKD1 (suppressor of potassium transport growth defect) belongs to the AAA-ATPase family and is one of the class E VPS (vacuolar protein sorting) proteins. The ATPase activity-deficient form of SKD1 leads the perturbation of mechanism transport through endosomes and lysosomes, however, the molecular mechanism behind the action of SKD1 is poorly understood. In this study, it is identified that VPS4_YEAST (Saccharomyces cerevisiae) is the homology protein of mcSKD1 (Mesembryanthemum crystallinum SKD1) employing sequence profile analysis. The full-length mcSKD1 protein possesses MIT, AAA-ATPase, and NACHT domains of VPS4_YEAST. It is investigated that VPS4_YEAST (NACHT domain) interacts to BRO1_YEAST (HEAT repeat), BRO1_YEAST (HEAT repeat) to AIP1_YEAST (WD40 repeat), AIP1_YEAST (WD40 repeat) to ABP1_YEAST (ADF domain), ABP1_YEAST (ADF domain) to ARP2_YEAST (ACTIN domain), respectively, from yeast two-hybrid system via protein-protein interaction. These proteins employ the function of cytoskeleton structural proteins in cells. Hence, mcSKD1 protein may involve the mechanisms of potassium ion uptake and salt tolerance via the function of cytoskeleton structural proteins.
中文摘要・・・・・・・・・・・・・・・・・・・・・・・・・.6
英文摘要・・・・・・・・・・・・・・・・・・・・・・・・・.7
一、前言・・・・・・・・・・・・・・・・・・・・・・・・・・・.8
1-1冰花SKD1基因的相關實驗・・・・・・・・・・・・・・・・・.8
1-2酵母菌雙雜合系統是蛋白質-蛋白質交互作用預測的依據・・・・・10
二、研究方法與材料・・・・・・・・・・・・・・・・・・・・・・12
2-1蛋白質序列輪廓分析・・・・・・・・・・・・・・・・・・・・12
2-2研究方法・・・・・・・・・・・・・・・・・・・・・・・12
2-3酵母菌雙雜合系統蛋白質-蛋白質交互作用・・・・・・・・・・15
三、結果與討論・・・・・・・・・・・・・・・・・・・・・・・・・17
3-1冰花SKD1蛋白質的一級結構分析・・・・・・・・・・・・・・・17
3-1-1冰花SKD1的MIT domain分析・・・・・・・・・・・・・・18
3-1-2冰花SKD1的AAA ATPase domain分析・・・・・・・・・・20
3-1-3全長mcSKD1的domains分析・・・・・・・・・・・・・・・・28
3-1-4酵母菌系統的同源蛋白質──VPS4_YEAST(END13)・・・・・・・41
3-1-5冰花SKD1蛋白質具有NACHT domain的特徵・・・・・・・44
3-2全長冰花SKD1蛋白質的二級、三級結構預測・・・・・・・・・・・・47
3-2-1冰花SKD1蛋白質MIT domain的二級、三級結構預測・・・・・・・・47
3-2-2冰花SKD1蛋白質AAA ATPase domain的二級、三級結構預測・・・・49
3-3與VPS4_YEAST交互作用的蛋白質預測・・・・・・・・・・・・・・52
四、結論・・・・・・・・・・・・・・・・・・・・・・・・・・・・・・57
五、參考文獻・・・・・・・・・・・・・・・・・・・・・・・・・・・・59
1.何孟純(2002)利用酵母菌互補試驗探討mcSKD1基因鉀離子吸收機制及細胞耐鹽性,中興大學植物學研究所碩士論文。
2.周映孜(2002)鹽逆境下高等植物鉀鈉離子平衡及相關基因表現之分析,中興大學植物學研究所碩士論文。
3.Adams P.﹐Nelson D.E.﹐Yamada S.﹐Chmara W.﹐Jensen R.G.﹐Bohnert H.J. ,Griffiths H.(1998)Growth and development of Mesembryanthemum crystallinum(Aizoaceae)﹒New Phytol. 138, 171–190.
4.Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25, 3389-3402.
5.Aravind L., Koonin E.V. (2001) The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol. 2:RESEARCH0007. (Epub).
6.Ciccarelli F.D., Proukakis C., Patel H., Cross H., Azam S., Patton M.A., Bork P., Crosby A.H. (2003) The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia. Genomics 81, 437-441.
7.Confalonieri F., Duguet M. (1995) A 200-amino acid ATPase module in search of a basic function. Bioessays. 17, 639-650.
8.Crushman J.C.﹐Michaalowski C.B.﹐Bohnert H.J.(1990)Development control of Crassulacean acid metabolism inducibility by salt stress in the common ice plant. Plant Physiol. 94, 1137–1142.
9.Dever T.E., Glynias M.J., Merrick W.C. (1987) GTP binding domain: three consensus sequence elements with distinct spacings. Proc. Natl. Acad. Sci. USA. 84, 1814-1818.
10.Deng M., Sun F., Chen T. (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pac. Symp. Biocomput. 140-151.
11.Edwards G.E.﹐Dai Z.﹐Cheng S.-H.﹐Ku M.S.B.(1996)Factors effecting the induction of Crassulacean acid metabolism in Mesembryanthemum crystallinu﹒In Crassulacean Acid Metabolism﹕Biochemistry﹐ Ecophysiology and Evolution. Edited by Winter﹐K.﹐Smith﹐J.A.C. pp. 119–134. Ecological Studies﹐Vol. 114﹐Springer–Verlag﹐Berlin.
12.Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., Bairoch A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235-238.
13.Fields S., Sternglanz R. (1994) The two-hybrid system: an assay for protein-protein interactions. Trends Genet. 10, 286-292.
14.Fry D.C., Kuby S.A., Mildvan A.S. (1986) ATP-binding site of adenylate kinase: mechanistic implications of its homology with ras-encoded p21, F1-ATPase, and other nucleotide-binding proteins. Proc. Natl. Acad. Sci. U.S.A. 83, 907-911.
15.Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., Remor M., Hofert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M.A., Copley R.R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., Superti-Furga G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
16.Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Aca. Sci. USA. 98, 4569-4574. (Epub)
17.Koonin E.V. (1993) A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif. J. Mol. Biol. 229, 1165-1174.
18.Koonin E.V., Aravind L. (2000) The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci. 25, 223-224.
19.Letovsky S, Kasif S. (2003) Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics. 19 Suppl 1:i197-204.
20.Letunic I., Copley R.R., Schmidt S., Ciccarelli F.D., Doerks T., Schultz J., Ponting C.P., Bork P. (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res. 32 Database issue: D142-144.
21.Moller W., Amons R. (1985) Phosphate-binding sequences in nucleotide-binding proteins. FEBS Lett. 186, 1-7.
22.Neuwald A.F., Aravind L., Spouge J.L., Koonin E.V. (1999) AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27-43.
23.Patel H., Cross H., Proukakis C., Hershberger R., Bork P., Ciccarelli F.D., Patton M.A., McKusick V.A., Crosby A.H. (2002) SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia. Nat Genet.31, 347-348. (Epub)
24.Perier F.﹐Coulter K.L.﹐Liang H.﹐Radeke C.M.﹐Gaber G.F.﹐Vandenberg C.A.(1994) Identification of a novel mammalian member of the NSF/CDC48p/Pas1p/TBP-1 family through heterologous expression. FEBS Letters 351, 286–290.
25.Phillips S.A., Barr V.A., Haft D.H., Taylor S.I., Haft C.R. (2001) Identification and characterization of SNX15, a novel sorting nexin involved in protein trafficking. J. Biol. Chem 276, 5074-5084.
26.Phizicky E.M., Fields S. (1995) Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94-123.
27.Saraste M., Sibbald P.R., Wittinghofer A. (1990) The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15, 430-434.
28.Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M., Johnston M., Fields S., Rothberg J.M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
29.Uetz P., Hughes R.E. (2000) Systematic and large-scale two-hybrid screens. Curr. Opin. Microbiol. 3, 303-308.
30.Walhout A.J., Vidal M. (2001) High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24, 297-306.
31.Walker J.E., Saraste M., Runswick M.J., Gay N.J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1, 945-951.
32.Yen H.E.﹐Wu S.M.﹐Hung Y.H.﹐Yen S.K. (2000)Isolation of three salt-induced low-abundance cDNAs from light–grown callus of Mesembryanthemum crystallinum by suppression subtractive hybridization Physiol. Plant 110, 402–409.
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