利用3D分子模擬軟體預測竹筍蛋白質相似結構及功能

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姓名

蔡嘉志(CHIA-CHIH TSAI) 查詢紙本館藏

畢業系所

電機工程學系

論文名稱

利用3D分子模擬軟體預測竹筍蛋白質相似結構及功能
(Predict protein structure and similar function via 3D Visualization tools-case study of bamboo shoot)

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摘要(中)

虛擬預測結構的電腦繪圖軟體對這個研究是不可欠缺的工具,在分子生物學中,單單從一級結構(也就是胺基酸序列)而可以預測其三維的結構是一個尚未克服及非常重要的問題。
預測蛋白質的結構問題在分子生物學上扮演一個非常重要的角色,本論文研究目的在利用電腦的3D軟體預測竹筍蛋白質相似結構及功能。作者是用同源模擬法的原理來預測竹筍蛋白質的相似結構和討論其功能,並比較其差異性,這種模擬法讓我們更加瞭解竹筍蛋白質結構的特性並在預測蛋白質三級結構方面能有所突破。
本研究利用暑假台大生計中心提供之竹筍二維蛋白質電泳實驗,得到不同階段竹筍蛋白質序列,並且用BLAST和SAS去分析竹筍在出土前、出土後10cm、出土後30cm不同階段的相似序列及探討蛋白質其差異性。
最後,作者使用方式是和現今存在PDB資料庫中的結構作比較並利用相關分子模擬軟體(RasMol,Chime…等)來預測竹筍蛋白質的相似結構和討論其功能的差異性,而以即時三維虛擬分子模型視窗的網頁方式呈現出來。

摘要(英)

Computer graphical methods of visualizing structures are important tools in this research. This prediction of protein three dimensional conformations from the primary structure (i.e. amino-acid sequence) is one of the important unsolved problems in molecular biology.
The purpose of this research is to predict the similar protein structure and its function for bamboo shoot by computational technology with 3D computer software. The reason for predict a protein structure that it plays an important role in molecular biology. In this paper, the author attempted to predict a protein structure of bamboo shoot that discusses similar function and can be used in homology modeling. This method provides a substantial increase in understanding of protein structural features, knowledge about which will assist in prediction work.
The research uses three sequence samples of bamboo shoot from the department of Biotechnology, National Taiwan University at summer biotechnology at experimental courses in 2003 year. The author analyze the three types (there are Native, have come out of Ground at 10cm and 30cm) via BLAST and SAS bioinformatics websites.
Finally, the author can use tools (RasMol, Chime…) to predict bamboo shoot similar protein structure and discuss its function comparing with current PDB database structures that it can show web-base by Internet + 3D Visualization Real-time Molecular viewer.

關鍵字(中)

★ 蛋白質結構
★ 蛋白質折疊

關鍵字(英)

★ protein folding
★ protein structure
★ 3D computer software

論文目次

Chapter 1 Introduction ………………………………………………1
1.1 Motivation.…….…………………………………………………………1
1.2 Literature survey and Related work……………………………………2
1.3 Merits and Contribution…………………………………………………4
1.4 Organization of the Thesis ………………………………………………4
Chapter 2 Protein Database and Visualization Structure………….5
2.1 Amino Acids and Peptide……………..…………………………………..5
2.2 Protein and Experiment of Protein Series………………………………8
2.3 Protein Database (PDB) and PDBsum…………………………………11
2.4 Pairwise Alignment Technique (BLAST and FASTA)………………15
2.5 SCOP and CATH Tools………………………………………………….19
2.6 RasMol and RasMol Based Viewers…………………………………….21
2.7 The Folding Problem of Structure………………………………………..24
Chapter 3 Similar Protein Structure Survey………………………26
3.1 System Architecture…….………………………………………………..26
3.2 Characteristic of Bamboo Shoot’s Protein series……………………30
3.3 Comparison of Different Methods……………………………………….31
3.4 Results of Related PDB and Ramachandram Plot………………………35
3.5 Results of SCOP and CATH…………………………………………..37
Chapter 4 Similar Protein Structure Analysis…………………….44
4.1 Secondary Structure of Similar Protein………………………………….44
4.2 The Hydrophobic Effect of Similar Protein……………………………..52
4.3 Results of Protein Structures by RasMol………………………………64
4.4 Predict Similar Structure andFunction…………………………………..67
Chapter 5: Conclusion and Future Work ………………………….73
Reference ………...…………………………………………………74

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[55] 基礎生物資訊實務　李炎編著

指導教授

歐石鏡(Shin-Ching Ou)

審核日期

2004-7-2

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