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研究生:謝濟安
論文名稱:利用演化樹追蹤法分析TIMBarrel中配醣酶家族的聚醣
論文名稱(外文):Evolutionary Trace Analysis of Beta-Glycanase in (Trans) Glycosidase Superfamily Adopting TIM Barrel Fold
指導教授:唐傳義
學位類別:碩士
校院名稱:國立清華大學
系所名稱:資訊工程學系
學門:工程學門
學類:電資工程學類
論文種類:學術論文
論文出版年:2004
畢業學年度:92
語文別:英文
論文頁數:27
中文關鍵詞:演化樹演化樹追蹤蛋白質演化蛋白質功能
外文關鍵詞:evolution treeTIM Barrelevolutionary traceGlycosidase
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Abstract
To predict the protein binding domain or active site residues of an enzyme always helps offering useful information for protein and enzyme researches.A strategy called “Evolutionary Trace Method (denoted to ET)” is developed by Lichtarge et al. (1996). We try to use ET to investigate TIM barrel glycosidase superfamily. The diversity within the samples is so enormous that many gaps occur during MSA. To handle this problem, we modify Evolutionary Trace by tracing consensus of protein groups belonged to “the same ancestor” by each level of tree instead of according “PICs”, partition identity cutoffs (PICs) that are used to define partitions. Our Evolutionary Trace Method is compared to traditional one by repeat experiment made by Mathew E. Sowa et al. . Six residues with PDEγ effects identified by Mathew E. Sowa et al. are identified on branch 12 in our studies, too. No false negative result occurs in our study. Then we investigate beta-glycanases TIM-barrel in glycosidases superfamily. Among 313 residues of Cellulose/Xylan Specificity of the beta-1,4-Glycanase Cex from Cellulomonas fimi[1exp], we can eliminate 281 unnecessary residues from 313 residues of Cellulose/Xylan Specificity of the beta-1,4- Glycanase Cex from ellulomonas fimi and pick up 32 critical residues on branch 39. Ten of picked up residues are considered to play a role in hydrolase activities. In contrast, traditional Evolutionary Trace can get no information.

This is helpful to biologists, and they can save a lot of time and money. This is the contribution of our modified Evolutionary Trace Method.
Table of Contents

Abstract……………………………………………….. 0
致謝…………………………………………………… 0
Table of Contents……………………………………… I
List of Figures………………………………………… II
List of Tables…………………………………………. III
Chapter 1 Introduction………………………………... 1
Chapter 2 Background and previous studies…………...4
2.1 TIM-barrel……………………………….4
2.2 (Trans)glycosidases Superfamily………..5
2.3 Evolutionary Trace Method……………..6
Chapter 3 Materials And Methods…………...………. 11
3.1 Samples……………...………………… 11
3.2 System and Methods..…………………. 12
Chapter 4 Experimental Results and Discussion…….. 19
4.1 Regulator of G protein signaling(RGS) family………………………………….19
4.2 (Trans)glycosidases Superfamily……... 22
Chapter 5 Conclusion…………………………………25
Reference……………………………………………...26


List of Figures

Fig. 1 The topology diagram of Hevamine-one of the TIM barrel structures……………………………………………………… 4
Fig.2 Glycosides are composed of two structural features………..…. 5
Fig.3 The role of glycosidases is the hydrolysis of the sugar-aglycon bond………………………………….……..…………..…..…..6
Fig.4. partition identity cutoffs (PICs)………………..…………………………….. 8
Fig.5 Derivation of the evolutionary trace……………..…………….. 9
Fig.6 ET of the RGS protein family………………………………… 20
Fig.7 Evolutionary Tree and tracing pathway……………..…………21
Fig.8 Evolutionary Tree constructed in case of our study…………....23






List of Tables

Table1. List of beta-glycanases of TIM-barrel glycosidases……...…... 18
Table 2. Correlation of ET identified RGS residues with PDE….…… 20
Reference
[1]Farber,G.K. (1993) An tim barrel full of evolutionary trouble. Current Opinion in Structural Biology, 3, 409-412.
[2]Henrissat,B. and Davies,G. (1997) Current Opinion in Structural Biology, 7, 637-644.
[3]Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
[4]Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method de.nes binding surfaces common to protein families. J Mol Biol 1996;257:342–358.
[5]Higgins D., Thompson J., Gibson T. Thompson J. D., Higgins D. G., Gibson T.J.(1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
[6]Mathew E.Sowa, Wei He et al. (2000) A regulator of G protein signaling interaction surface linked to effector specificity. PNAS. Vol.97 no.4 :1483-1488
[7]Umesh R Desai, Ph.D.Associate. School of Pharmacy, Virginia Commonwealth University, Richmond, VA http://www.people.vcu.edu/~urdesai/
[8]Biocatalysis page. Wageningen University 2001 http://www.ftns.wau.nl/oc/research/biocatalysis/glycosidase/glycosidasepage.htm
[9]Chothia, C. & Lesk, A. M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823–826.
[10]Zvelebil, M. J., Barton, G. J., Taylor, W. R. & Sternberg, M. J. (1987). Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195, 957–961.
[11]Shunyi Zhu, Isabelle Huys et al.(2004) Evolutionary Trace Analysis of Scorpion Toxins Specific for K-Channels. PROTEINS: Structure, Function, and Bioinformatics 54:361-370
[12]Wang, J., Ducret, A. T. Y., Kozasa, T., Aebersold, R. & Ross, E. M. (1998) J. Biol. Chem. 273, 26014–26025.
[13]Hepler, J. R., Berman, D. M., Gilman, A. G. & Kozasa, T. (1997) Proc. Natl. Acad. Sci. USA 94, 428–432.
[14]O’Neill, G., Goh, S. H., Warren, R. A. J., Kilburn, D. G., and Miller, R. C., Jr. (1986) Gene 44, 325.
[15]A.White, D.Tull, et al.(1996).Crystallographic observation of a covalent catalytic intermediate in a beta-glycosidase. Nat Struct Biol. Feb;3(2):149-54.
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