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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 王勝仕 | |
| dc.contributor.author | Yao-Zong Chen | en |
| dc.contributor.author | 陳耀宗 | zh_TW |
| dc.date.accessioned | 2021-06-16T06:33:46Z | - |
| dc.date.available | 2019-08-14 | |
| dc.date.copyright | 2014-08-14 | |
| dc.date.issued | 2014 | |
| dc.date.submitted | 2014-08-04 | |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/57053 | - |
| dc.description.abstract | 對於蛋白質的結構有更深入的了解有助於引導誘變實驗設計,而誘變實驗可 以探討與證實結構與功能之間的相關性,在發展新的疾病療法上有相當程度的幫 助。同源模擬法(homology modeling)是一種電腦模擬方法用於蛋白質結構預測,從 具有同源性蛋白質之現存解出結構(可能由 NMR 或 X-ray diffraction 得到)為模板, 模擬出未知序列的蛋白質結構。該方法立基於觀察到蛋白質三級結構和一級結構 相較之下更為保守,因此兩個蛋白質即使在序列下有較大落差,還是有可能存在 相同的折疊方式。同源模擬方法的主要步驟為選擇模板、排比、主鏈與側鏈預測、 結構最佳化及模型評估。模板的選擇最為重要,與能否模擬出正確的結構有很大 關聯;排比是將目標序列與未知序列調整至兩者對應到最佳的同源區域;模型的 主鏈原子將對應到模板的三維結構,因此不保守的側鏈方向也會被預測出來;最 佳化則是透過力場模擬立體空間的障礙,改善原子間的氫鍵作用力關係;最後對 最終模型評估其正確性,找出模型中出現錯誤的區域;而如非保守型的 loop 二級 結構,則需要和保守型區域獨立開來模擬。本研究之實驗分為四個獨立的流程, 包含 SWISS-MODEL 自動化同源模擬、SWISS-pdbviewer、Modeller、BAM 模擬 流程,嘗試得到抗菌胜肽—天蠶素 cecropin a 的三級結構,其中由 BAM 流程分別 基於 1F0H、1D9J、2LA2 等三個模板建構而得之模型,在 GA341 的評分標準下, 符合蛋白質的正確摺疊。本研究提供不同模擬流程的比較,建構出合理的模型。 | zh_TW |
| dc.description.abstract | Better understanding on protein structure can aid in designing mutagenesis experiments, leading to verification of the structure–function relationships and even facilitating the development of new therapeutics for diseases. Homology modelling is an in silico simulation method for protein structure prediction. Modeling structure of query amino acid sequence is based on a homologous template structure experimentally solved by NMR or X-ray diffraction. The construction of homology modelling is based upon the observation that the tertiary structure of proteins is more conserved than their primary structure. This can be used to explain the fact that even two proteins with distinct primary structures may still share the same folding behavior.
The key steps in homology modelling are template selection, alignment, backbone and side-chain prediction, structure optimization and model evaluation. The crucial step is template choosing. Inappropriate selection would result in incorrect structures. The purpose of alignment step aims at adjusting the alignment to ensure that the sequences fit optimal correspondence between the homologous regions. In the next step, the backbone atoms of model would be translated to fit the tertiary structure of the template, and the non-conservative side-chains can then be predicted. The optimization step serves to remove the steric clashes and hydrogen-bonding relations between atoms. Finally, the correctness of the model is evaluated and the errors in the model are determined. The non-conservative loops and the conservative regions may be modelled separately. In this thesis, attempt was made to model the tertiary structure of a 37-residue antimicrobial peptide cecropin A using four different methods, including SWISS-MODEL, SWISS-pdb viewer, modeler, and BAM. Through BAM process, we obtained three reliable structures which were built upon the templates of 1F0H, 1D9J, and 2LA2 according to the GA341 scoring critera. In this research, the reliable models were built by comparing different modelling processes. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T06:33:46Z (GMT). No. of bitstreams: 1 ntu-103-R01524085-1.pdf: 4858458 bytes, checksum: 541e9f5fae4e917dffe742b1abe4e519 (MD5) Previous issue date: 2014 | en |
| dc.description.tableofcontents | 摘要 I
ABSTRACT II 目錄 IV 圖目錄 VII 表目錄 X 第一章 序論 1 1.1前言 1 1.2 研究目的 2 第二章 文獻回顧 3 2.1蛋白質結構概述 3 2.1.1蛋白質結構層次 3 2.1.2蛋白質結構的測定方法 7 2.1.3生物資料庫 10 2.1.4蛋白質結構預測 12 2.1.5二級結構預測理論 19 2.1.6二級結構預測工具 20 2.2抗菌胜肽 (ANTIMICROBIAL PEPTIDES) 22 2.2.1抗菌胜肽簡介 22 2.2.2抗菌胜肽類別 23 2.2.3抗菌機制 25 2.2.4 天蠶素(cecropin)之簡介 32 2.3 同源模擬法 (HOMOLOGY MODELING METHOD) 37 2.3.1同源模擬法原理 37 2.3.2同源模擬預測蛋白質的基本步驟 39 2.3.3生物資訊學簡介 42 2.3.4自動化模擬(automated modelling)簡介 48 2.3.5 SWISS-MODEL簡介 51 2.3.6 模型品質評估 54 第三章 實驗儀器與步驟 58 3.1實驗軟體與伺服器 58 3.1.1 BioAssemblyModeler 58 3.1.2 Scrwl4 58 3.1.3 UCSF Chimera 59 3.1.4 Modeller 59 3.2軟體安裝與設定 60 3.3同源模擬步驟 65 3.3.1 Modeller模擬流程 65 3.3.2 BAM模擬流程 66 第四章 結果與討論 79 4.1 QMEAN Z-SCORE分析 79 4.1.1 SWISS-MODEL結果分析 80 4.1.2 SWISS-pdbviewer結果分析 85 4.2 GA341分析 90 4.2.1 Modeller結果分析 92 4.2.2 SWISS-MODEL結果分析 95 4.2.3 BAM結果分析 96 4.3 結果討論 99 第五章 未來展望 103 附錄 104 附錄A SWISS-MODEL操作流程 104 附錄B KOBAMIN 107 附錄C 圖檔對照表 109 參考文獻 111 | |
| dc.language.iso | zh-TW | |
| dc.subject | SWISS-MODEL | zh_TW |
| dc.subject | 同源模擬法 | zh_TW |
| dc.subject | cecropin a | zh_TW |
| dc.subject | 蛋白質結構預測 | zh_TW |
| dc.subject | 抗菌胜? | zh_TW |
| dc.subject | SWISS-pdbviewer | zh_TW |
| dc.subject | BAM | zh_TW |
| dc.subject | Modeller | zh_TW |
| dc.subject | antimicrobial peptides | en |
| dc.subject | SWISS-MODEL | en |
| dc.subject | Modeller | en |
| dc.subject | BAM | en |
| dc.subject | SWISS-pdbviewer | en |
| dc.subject | cecropin A | en |
| dc.subject | prediction of protein structure | en |
| dc.subject | homology modelling | en |
| dc.title | 以同源模擬法預測天蠶素結構 | zh_TW |
| dc.title | Cecropin A Structure Prediction Using Homology Modelling | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 102-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 陳美娥,吳宛儒,林達顯,侯劭毅 | |
| dc.subject.keyword | 同源模擬法,蛋白質結構預測,抗菌胜?,SWISS-MODEL,Modeller,BAM,SWISS-pdbviewer,cecropin a, | zh_TW |
| dc.subject.keyword | homology modelling,prediction of protein structure,antimicrobial peptides,SWISS-MODEL,Modeller,BAM,SWISS-pdbviewer,cecropin A, | en |
| dc.relation.page | 119 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2014-08-04 | |
| dc.contributor.author-college | 工學院 | zh_TW |
| dc.contributor.author-dept | 化學工程學研究所 | zh_TW |
| 顯示於系所單位： | 化學工程學系 | |
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