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請用此 Handle URI 來引用此文件: http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/30042
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dc.contributor.advisor林榮信
dc.contributor.authorShu-Hao Yehen
dc.contributor.author葉書豪zh_TW
dc.date.accessioned2021-06-13T01:32:22Z-
dc.date.available2009-08-08
dc.date.copyright2007-08-08
dc.date.issued2007
dc.date.submitted2007-07-17
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3. Klebe, G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discovery Today 11, 580-594 (2006).
4. Brenk, R., Irwin, J.J. & Shoichet, B.K. Here Be dragons: Docking and screening in an uncharted region of chemical space. Journal of Biomolecular Screening 10, 667-674 (2005).
5. Shoichet, B.K. Virtual screening of chemical libraries. Nature 432, 862-865 (2004).
6. Kubinyi, H. Success Stories of Computer-Aided Design. in Computer Applications in Pharmaceutical Research and Development (ed. Ekins, S.) 377-424 (Wiley-Interscience, 2006).
7. Fornabaio, M., et al. Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes. Journal of Medicinal Chemistry 47, 4507-4516 (2004).
8. Chen, Z.G., et al. Crystal-Structure at 1.9-Angstrom Resolution of Human-Immunodeficiency-Virus (Hiv)-Ii Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the Hiv Proteases. Journal of Biological Chemistry 269, 26344-26348 (1994).
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10. Herron, D.K., et al. 1,2-dibenzamidobenzene inhibitors of human factor Xa. Journal of Medicinal Chemistry 43, 859-872 (2000).
11. Yee, Y.K., et al. N-2-aroylanthranilamide inhibitors of human factor Xa. Journal of Medicinal Chemistry 43, 873-882 (2000).
12. Rarey, M., Kramer, B. & Lengauer, T. The particle concept: Placing discrete water molecules during protein-ligand docking predictions. Proteins-Structure Function and Genetics 34, 17-28 (1999).
13. Verdonk, M.L., et al. Modeling water molecules in protein-ligand docking using GOLD. Journal of Medicinal Chemistry 48, 6504-6515 (2005).
14. Friesner, R.A., et al. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry 47, 1739-1749 (2004).
15. Pitt, W.R. & Goodfellow, J.M. Modeling of Solvent Positions around Polar Groups in Proteins. Protein Engineering 4, 531-537 (1991).
16. Goodford, P.J. A Computational-Procedure for Determining Energetically Favorable Binding-Sites on Biologically Important Macromolecules. Journal of Medicinal Chemistry 28, 849-857 (1985).
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18. Verdonk, M.L., Cole, J.C. & Taylor, R. SuperStar: A knowledge-based approach for identifying interaction sites in proteins. Journal of Molecular Biology 289, 1093-1108 (1999).
19. Kortvelyesi, T., Dennis, S., Silberstein, M., Brown, L. & Vajda, S. Algorithms for computational solvent mapping of proteins. Proteins-Structure Function and Genetics 51, 340-351 (2003).
20. Nissink, J.W.M., et al. A new test set for validating predictions of protein-ligand interaction. Proteins-Structure Function and Genetics 49, 457-471 (2002).
21. Khandelwal, A., et al. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. Journal of Medicinal Chemistry 48, 5437-5447 (2005).
22. Dudev, T. & Lim, C. Factors governing the protonation state of cysteines in proteins: An ab initio/CDM study. Journal of the American Chemical Society 124, 6759-6766 (2002).
23. Sakharov, D.V. & Lim, C. Zn protein simulations including charge transfer and local polarization effects. Journal of the American Chemical Society 127, 4921-4929 (2005).
24. Morris, G.M., et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 19, 1639-1662 (1998).
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29. Dolinsky, T.J., Nielsen, J.E., McCammon, J.A. & Baker, N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research 32, W665-W667 (2004).
30. Li, H., Robertson, A.D. & Jensen, J.H. Very fast empirical prediction and rationalization of protein pK(a) values. Proteins-Structure Function and Bioinformatics 61, 704-721 (2005).
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33. MacKerell, A.D., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102, 3586-3616 (1998).
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37. Kim, E.E., et al. Crystal-Structure of Hiv-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme. Journal of the American Chemical Society 117, 1181-1182 (1995).
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39. Champness, J.N., et al. Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands. Proteins-Structure Function and Genetics 32, 350-361 (1998).
40. Sleigh, S.H., Seavers, P.R., Wilkinson, A.J., Ladbury, J.E. & Tame, J.R.H. Crystallographic and calorimetric analysis of peptide binding to OppA protein. Journal of Molecular Biology 291, 393-415 (1999).
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dc.identifier.urihttp://tdr.lib.ntu.edu.tw/jspui/handle/123456789/30042-
dc.description.abstract水分子與金屬離子在生物巨分子的結構或功能上扮演重要的角色。水分子可以與蛋白質或小分子形成氫鍵而介入其二者之間的交互作用,並且在許多研究報告當中指出,水分子在蛋白質與小分子的分子嵌合模擬當中具有巨大的影響力。因此在分子嵌合模擬方法的開發當中,如何適當地考慮水分子便成為一個相當重要的議題。
金屬離子如鋅、錳、鐵、銅在許多金屬蛋白中通常扮演著輔因子的角色,並且要使金屬蛋白的催化機轉得以正常運作,它們必須存在。在其他方面,金屬離子也可以穩定像蛋白質或核糖核酸等巨分子的結構,而使它們能夠正常地作用。許多金屬蛋白是重要的藥物作用標的,也因此使得在分子嵌合模擬當中能夠更適當地考慮金屬離子是必要的。然而,將小分子嵌入含有金屬離子的活性位置仍是一件具有相當挑戰性的工作。這是由於配位數的變異性、以及缺少可以精確描述小分子與金屬離子之間作用力的分子力場參數所致。
在此我們發展出一個具有一般性的方法,用在蛋白質與小分子的嵌合模擬中適當地考慮水分子,以及用電荷轉移效應來更精確地描述小分子與金屬離子之間的作用力,而非如一般分子嵌合方法中將電荷視為固定值。
zh_TW
dc.description.abstractWater and metal ions are important molecules that act structurally or functionally in macromolecules. Water molecules can be involved in the interaction between protein and ligand by forming hydrogen bonds, and many researches have been reported that sometimes they are crucial in docking studies. Therefore it makes the development of docking method which can consider water molecules explicitly to be an important issue.
Metal ions, such like zinc, manganese, iron, and copper, are often act as metal cofactors in many metalloproteins and are crucial for their normal catalytic mechanism. In other cases, they can also stabilize the structure of macromolecules such as proteins or RNAs for normal function. Many metalloproteins are important drug targets, and hence there is a necessity to consider these metal ions more properly in molecular docking studies. However, docking ligands into metal-containing active site is still a challenging work because the varieties of coordination numbers and the lack of accurate force field parameters to describe the ligand-metal interaction.
Here we develop a general method to consider the water explicitly, and at the same time the interaction between ligand and metal ions are considered more deliberately by introducing charge transfer effect in protein-ligand docking instead of static partial charges model in general docking methods.
en
dc.description.provenanceMade available in DSpace on 2021-06-13T01:32:22Z (GMT). No. of bitstreams: 1
ntu-96-R94423004-1.pdf: 2531822 bytes, checksum: f6a452e6be7ca1638b90c45b94ff0428 (MD5)
Previous issue date: 2007
en
dc.description.tableofcontents口試委員會審定書 ii
誌謝 iii
Table of Contents iv
Figure List vii
Table List ix
中文摘要 x
Abstract xi
Chapter 1: Introduction 1
1.1 Virtual Screening 1
1.2 The Importance of Water in Docking Studies 3
1.3 SuperStar: Prediction of Potential Water Binding Sites 4
1.4 The Importance of Metal Ions in Docking Studies 5
1.5 AutoDock 3.0.5 and Its Scoring Function 7
Chapter 2: Material and Methods 10
2.1 Protein-Ligand File Preparation 10
2.1.1 Ligand File Preparation for AutoDock 10
2.1.2 Protein File Preparation for AutoDock 11
2.1.3 Parameters Used in AutoDock_3.0.5 13
2.2 AutoDock_3.0.5 with Variable Water Molecules 13
2.3 AutoDock_3.0.5 with Charge Transfer Effect 15
2.4 Preparing the Water Molecules and Metal Ions for Modified AutoDock_3.0.5 18
2.4.1 PDB2PQR 18
2.4.2 SuperStar 19
2.4.3 Autogrid3 20
2.4.4 Autodock3 20
Chapter 3: Results 24
3.1 The Assignment of Crystal Water Orientation 24
3.1.1 HIV-1 Protease (PDBID: 1HPV) 25
3.1.2 Factor Xa (PDBID: 1F0R) 27
3.1.3 Thymidine kinase (PDBID: 1KIM) 28
3.1.4 Oligopeptide-binding protein OppA (PDBID: 1B5I) 28
3.1.5 The Binding Energy of the Crystallographic Binding Mode with or without Including Water Molecules 29
3.2 Consider Water Molecules as Rigid or Variable Ones in the Docking Procedure 30
3.2.1 HIV-1 Protease (PDBID: 1HPV) 31
3.2.2 Factor Xa (PDBID: 1F0R) 32
3.2.3 Thymidine kinase (PDBID: 1KIM) 33
3.2.4 Oligopeptide-binding protein OppA (PDBID: 1B5I) 34
3.3 Consider Charge Transfer Effect in Docking Procedure 35
Chapter 4: Discussion 65
4.1 The Assignment of Water Orientation in Docking Studies 65
4.2 The Performance 66
4.3 The Parameter Tuning of Charge Transfer Effect 66
References 69
dc.language.isoen
dc.title發展金屬蛋白系統之新穎分子嵌合方法zh_TW
dc.titleDeveloping a novel general-purposed docking scheme with explicit water and metal ions for metalloproteinsen
dc.typeThesis
dc.date.schoolyear95-2
dc.description.degree碩士
dc.contributor.oralexamcommittee許世宜,楊大衍,孫英傑
dc.subject.keyword分子嵌合,金屬蛋白,zh_TW
dc.subject.keyworddocking,metalloprotein,en
dc.relation.page74
dc.rights.note有償授權
dc.date.accepted2007-07-17
dc.contributor.author-college醫學院zh_TW
dc.contributor.author-dept藥學研究所zh_TW
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