請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/64682
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 陳平 | |
dc.contributor.author | Min-Fan Tang | en |
dc.contributor.author | 楊敏汎 | zh_TW |
dc.date.accessioned | 2021-06-16T22:57:21Z | - |
dc.date.available | 2017-08-28 | |
dc.date.copyright | 2012-08-28 | |
dc.date.issued | 2012 | |
dc.date.submitted | 2012-08-09 | |
dc.identifier.citation | 1.
Crick, F. Central Dogma of Molecular Biology. Nature 1970, 227, 561. 2. Mizutani, S.; Boettiger, D.; Temin, H. M. A DNA-depenent DNA olymerase and a DNA endonuclease in virions of Rous sarcoma virus. Nature 1970, 228, 424. 3. Temin, H. M.; Mizutani, S. RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature 1970, 226, 1211. 4. McCarthy, B. J.; Holland, J. J. Denatured DNA as a direct template for in vitro protein synthesis. Proc. Natl. Acad. Sci. U. S. A. 1965, 54, 880. 5. Burd, C. G.; Dreyfuss, G. Conserved structures and diversity of functions of RNA-binding proteins. Science 1994, 265, 615. 6. Brivanlou, A. H.; Darnell, J. E., Jr. Signal transduction and the control of gene expression. Science 2002, 295, 813. 7. Mermall, V.; Post, P. L.; Mooseker, M. S. Unconventional myosins in cell movement, membrane traffic, and signal transduction. Science 1998, 279, 527. 8. Cyster, J. G. Chemokines and cell migration in secondary lymphoid organs. Science 1999, 286, 2098. 9. Rudd, P. M.; Wormald, M. R.; Dwek, R. A. Glycosylation and the immune system. J. Protein Chem. 1998, 17, 519. 10. Marcotte, E. M.; Pellegrini, M.; Ng, H. L.; Rice, D. W.; Yeates, T. O.; Eisenberg, D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285, 751. 11. Palmer, C. N. A.; Irvine, A. D.; Terron-Kwiatkowski, A.; Zhao, Y. W.; Liao, H. H.; Lee, S. P.; Goudie, D. R.; Sandilands, A.; Campbell, L. E.; Smith, F. J. D.; O'Regan, G. M.; Watson, R. M.; Cecil, J. E.; Bale, S. J.; Compton, J. G.; DiGiovanna, J. J.; Fleckman, P.; Lewis-Jones, S.; Arseculeratne, G.; Sergeant, A.; Munro, C. S.; El Houate, B.; McElreavey, K.; Halkjaer, L. B.; Bisgaard, H.; Mukhopadhyay, S.; McLean, W. H. I. Common loss-of-function variants of the epidermal barrier protein filaggrin are a major predisposing factor for atopic dermatitis. Nat. Genet. 2006, 38, 441. 12. Engvall, E.; Ruoslahti, E. Binding of soluble form of fibroblast surface protein, fibronectin, to collagen. Int. J. Cancer 1977, 20, 1. 16 13. Goodsell, D. S.; Olson, A. J. Structural symmetry and protein function. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 105. 14. Wright, P. E.; Dyson, H. J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 1999, 293, 321. 15. Schellman, J. A.; Schellman, C. G. Kaj Ulrik Linderstrom-Lang (1896-1959). Protein Sci. 1997, 6, 1092. 16. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 1963, 7, 95. 17. L.Nelson, D.; Cox, M. M. Lehninger Principles of Biochemistry, Fourth edition. W,H, Freeman and Company: New York, 2005. 18. Palau, J.; Argos, P.; Puigdomenech, P. Protein secondary structure - studies on the limits of prediction accuracy. Int. J. Pept. Protein Res. 1982, 19, 394. 19. Hobohm, U.; Scharf, M.; Schneider, R.; Sander, C. Selection of representative protein data sets. Protein Sci. 1992, 1, 409. 20. Hobohm, U.; Sander, C. Enlarged representative set of protein structures. Protein Sci. 1994, 3, 522. 21. Griep, S.; Hobohm, U. PDBselect 1992-2009 and PDBfilter-select. Nucleic Acids Res. 2010, 38, D318. 22. Chou, P. Y.; Fasman, G. D. β-Τurns in proteins. J. Mol. Biol. 1977, 115, 135. 23. Pauling, L.; Corey, R. B.; Branson, H. R. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U. S. A. 1951, 37, 205. 24. Agawa, Y.; Lee, S.; Ono, S.; Aoyagi, H.; Ohno, M.; Taniguchi, T.; Anzai, K.; Kirino, Y. Interaction with phospholipid bilayers, ion channel formation, and antimicrobial activity of basic amphipathic alpha-helical model peptides of various chain lengths. J. Bio. Chem. 1991, 266, 20218. 25. Sansom, M. S.; Kerr, I. D.; Mellor, I. R. Ion channels formed by amphipathic helical peptides. A molecular modelling study. EBJ 1991, 20, 229. 26. Chasteen, N. D.; Harrison, P. M. Mineralization in ferritin: an efficient means of iron storage. J. Struct. Biol. 1999, 126, 182. 27. Fishburn, J.; Mohibullah, N.; Hahn, S. Function of a eukaryotic transcription activator during the transcription cycle. Mol. Cell 2005, 18, 369. 28. Hope, I. A.; Struhl, K. GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. The EMBO journal 1987, 6, 2781. 29. O'Shea, E. K.; Klemm, J. D.; Kim, P. S.; Alber, T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991, 254, 539. 30. Ogbay, B.; Dekoster, G. T.; Cistola, D. P. The NMR structure of a stable and compact all-β-sheet variant of intestinal fatty acid-binding protein. Protein Sci. 2004, 13, 1227. 31. Hashimoto, M.; Rockenstein, E.; Crews, L.; Masliah, E. Role of protein aggregation in mitochondrial dysfunction and neurodegeneration in Alzheimer's and Parkinson's diseases. Neuromolecular Med. 2003, 4, 21. 32. Chou, P. Y.; Fasman, G. D. Beta-Turns in Proteins. J. Mol. Biol. 1977, 115, 135. 33. Venkatachalam, C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968, 6, 1425. 34. Kanyo, Z. F.; Pan, K. M.; Williamson, R. A.; Burton, D. R.; Prusiner, S. B.; Fletterick, R. J.; Cohen, F. E. Antibody binding defines a structure for an epitope that participates in the PrPC-->PrPSc conformational change. J. Mol. Biol. 1999, 293, 855. 35. Sibanda, B. L.; Thornton, J. M. β-Ηairpin families in globular proteins. Nature 1985, 316, 170. 36. Dolgikh, D. A.; Gilmanshin, R. I.; Brazhnikov, E. V.; Bychkova, V. E.; Semisotnov, G. V.; Venyaminov, S.; Ptitsyn, O. B. Alpha-Lactalbumin: compact state with fluctuating tertiary structure? FEBS Lett. 1981, 136, 311. 37. Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133. 38. Perutz, M. F.; Rossmann, M. G.; Cullis, A. F.; Muirhead, H.; Will, G.; North, A. C. Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis. Nature 1960, 185, 416. 39. Nicholls, A.; Sharp, K. A.; Honig, B. Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins-Structure Function and Genetics 1991, 11, 281. 40. Perutz, M. F. Electrostatic effects in proteins. Science 1978, 201, 1187. 41. Rose, G. D.; Wolfenden, R. Hydrogen bonding, hydrophobicity, packing, and protein folding. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 381. 42. Pace, C. N. Evaluating contribution of hydrogen bonding and hydrophobic bonding to protein folding. Methods Enzymol. 1995, 259, 538. 43. Chothia, C. Hydrophobic bonding and accessible surface area in proteins. Nature 1974, 248, 338. 44. Wertz, D. H.; Scheraga, H. A. Influence of water on protein structure. An analysis of the preferences of amino acid residues for the inside or outside and for specific conformations in a protein molecule. Macromolecules 1978, 11, 9. 45. Guy, H. R. Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys. J. 1985, 47, 61. 46. Rees, D. C.; Adams, M. W. Hyperthermophiles: taking the heat and loving it. Structure 1995, 3, 251. 47. Vogt, G.; Woell, S.; Argos, P. Protein thermal stability, hydrogen bonds, and ion pairs. J. Mol. Biol. 1997, 269, 631. 48. Spassov, V. Z.; Karshikoff, A. D.; Ladenstein, R. The optimization of protein-solvent interactions: thermostability and the role of hydrophobic and electrostatic interactions. Protein Sci.1995, 4, 1516. 49. Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 1999, 289, 1435. 50. Horovitz, A.; Fersht, A. R. Strategy for Analyzing the Cooperativity of Intramolecular Interactions in Peptides and Proteins. J. Mol. Biol. 1990, 214, 613. 51. Schreiber, G.; Fersht, A. R. Energetics of Protein-Protein Interactions - Analysis of the Barnase-Barstar Interface by Single Mutations and Double Mutant Cycles. J. Mol. Biol. 1995, 248, 478. 52. Horovitz, A.; Serrano, L.; Avron, B.; Bycroft, M.; Fersht, A. R. Strength and co-operativity of contributions of surface salt bridges to protein stability. J. Mol. Biol. 1990, 216, 1031. 53. Takano, K.; Tsuchimori, K.; Yamagata, Y.; Yutani, K. Contribution of salt bridges near the surface of a protein to the conformational stability. Biochemistry 2000, 39, 12375. 54. Strop, P.; Mayo, S. L. Contribution of surface salt bridges to protein stability. Biochemistry 2000, 39, 1251. 55. Leeper, T. C.; Athanassiou, Z.; Dias, R. L.; Robinson, J. A.; Varani, G. TAR RNA recognition by a cyclic peptidomimetic of Tat protein. Biochemistry 2005, 44, 12362. Chapter2. 1. Hobohm, U.; Scharf, M.; Schneider, R.; Sander, C. Selection of representative protein data sets. Protein Sci. 1992, 1, 409. 2. Hobohm, U.; Sander, C. Enlarged representative set of protein structures. Protein Sci. 1994, 3, 522. 3. Griep, S.; Hobohm, U. PDBselect 1992-2009 and PDBfilter-select. Nucleic Acids Res. 2010, 38, D318. 4. Chothia, C. Conformation of twisted β leated sheets in proteins. J. Mol. Biol. 1973, 75, 295. 5. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 1963, 7, 95. 6. Richardson, J. S. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 1981, 34, 167. 7. Pan, K. M.; Baldwin, M.; Nguyen, J.; Gasset, M.; Serban, A.; Groth, D.; Mehlhorn, I.; Huang, Z. W.; Fletterick, R. J.; Cohen, F. E.; Prusiner, S. B. Conversion of α-helices into β-sheets features in the formation of the scrapie prion proteins. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 10962. 8. Smith, C. K.; Withka, J. M.; Regan, L. A thermodynamic scale for the β-sheet forming tendencies of the amino acids. Biochemistry 1994, 33, 5510. 9. Chou, P. Y.; Fasman, G. D. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 1974, 13, 211. 10. Levitt, M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978, 17, 4277. 11. Garnier, J.; Osguthorpe, D. J.; Robson, B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol. 1978, 120, 97. 12. Fasman, G. D. Protein conformational prediction. Trends Biochem. Sci. 1989, 14, 295. 13. Kim, C. A.; Berg, J. M. Thermodynamic β-sheet propensities measured using a zinc-finger host peptide. Nature 1993, 362, 267. 14. Minor, D. L.; Kim, P. S. Measurement of the β-Sheet-Forming Propensities of Amino-Acids. Nature 1994, 367, 660. 15. Krizek, B. A.; Amann, B. T.; Kilfoil, V. J.; Merkle, D. L.; Berg, J. M. A consensus zinc finger peptide - design, high-affinity metal-binding, a pH-dependent structure, and a his to Cys sequence variant. J. Am. Chem. Soc. 1991, 113, 4518. 16. Smith, C. K.; Withka, J. M.; Regan, L. A thermodynamic scale for the β-sheet forming tendencies of the amino-acids. Biochemistry 1994, 33, 5510. 17. Minor, D. L., Jr.; Kim, P. S. Measurement of the β-sheet-forming propensities of amino acids. Nature 1994, 367, 660. 18. Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. Elongation of the BH8 β-hairpin peptide: Electrostatic interactions in β-hairpin formation and stability. Protein Sci. 2001, 10, 1381. 19. Kiehna, S. E.; Waters, M. L. Sequence dependence of β-hairpin structure: comparison of a salt bridge and an aromatic interaction. Protein Sci. 2003, 12, 2657. 20. Ramirez-Alvarado, M.; Kortemme, T.; Blanco, F. J.; Serrano, L. β-Ηairpin and β-sheet formation in designed linear peptides. Biorg. Med. Chem. 1999, 7, 93. 21. Tatko, C. D.; Waters, M. L. The geometry and efficacy of cation-pi interactions in a diagonal position of a designed β-hairpin. Protein Sci. 2003, 12, 2443. 22. Ciani, B.; Jourdan, M.; Searle, M. S. Stabilization of β-hairpin peptides by salt bridges: Role of preorganization in the energetic contribution of weak interactions. J. Am. Chem. Soc. 2003, 125, 9038. 23. Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. Elongation of the BH8 β-hairpin peptide: Electrostatic interactions in β-hairpin formation and stability. Protein Sci. 2001, 10, 1381. 24. Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Chain reversals in proteins. Biochim. Biophys. Acta 1973, 303, 211. 25. Chou, P. Y.; Fasman, G. D. Prediction of protein conformation. Biochemistry 1974, 13, 222. 26. Lewis, P. N.; Momany, F. A.; Scheraga, H. A. Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proc. Natl. Acad. Sci. U. S. A. 1971, 68, 2293. 27. Chou, P.Y.; Fasman, G. D. β-Turns in proteins. J. Mol. Biol. 1977, 115, 135. 28. Venkatachalam, C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968, 6, 1425. 29. Hutchinson, E. G.; Thornton, J. M. A revised set of potentials for β-turn formation in proteins. Protein Sci. 1994, 3, 2207. 30. Imperiali, B.; Fisher, S. L.; Moats, R. A.; Prins, T. J. A Conformational study of peptides with the general structure Ac-L-Xaa-Pro-D-Xaa-L-Xaa-Nh2 - spectroscopic evidence for a peptide with significant β-turn character in water and in dimethyl-sulfoxide. J. Am. Chem. Soc. 1992, 114, 3182. 31. Haque, T. S.; Gellman, S. H. Insights on β-hairpin stability in aqueous solution from peptides with enforced type I' and type II' β-turns. J. Am. Chem. Soc. 1997, 119, 2303. 32. Ramirez-Alvarado, M.; Blanco, F. J.; Niemann, H.; Serrano, L. Role of β-turn residues in β-hairpin formation and stability in designed peptides. J. Mol. Biol. 1997, 273, 898. 33. Syud, F. A.; Espinosa, J. F.; Gellman, S. H. NMR-based quantification of β-sheet populations in aqueous solution through use of reference peptides for the folded and unfolded states. J. Am. Chem. Soc. 1999, 121, 11577. 34. Bolotina, I. A.; Chekhov, V. O.; Lugauskas, V.; Ptitsyn, O. B. [Determination of protein secondary structure from circular dichroism spectra. III. Protein-derived base spectra of circular dichroism for antiparallel and parallel β-structures]. Mol Biol 1981, 15, 167. 35. Sibanda, B. L.; Thornton, J. M. β-Hairpin Families in Globular-Proteins. Nature 1985, 316, 170. 37. Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 1989, 206, 759. 38. Wishart, D. S.; Sykes, B. D.; Richards, F. M. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 1991, 222, 311. 39. Szilagyi, L.; Jardetzky, O. α-Proton chemical-shifts and secondary structure in proteins. J. Magn. Reson. 1989, 83, 441. 40. Wishart, D. S.; Sykes, B. D.; Richards, F. M. The Chemical-shift index - a fast and 83 simple method for the assignment of protein secondary structure through NMR-spectroscopy. Biochemistry 1992, 31, 1647. 41. Bundi, A.; Wuthrich, K. H-1-Nmr Parameters of the common amino-acid Residues measured in aqueous-solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 1979, 18, 285. 42. Merutka, G.; Dyson, H. J.; Wright, P. E. 'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR 1995, 5, 14. 43. Wishart, D. S.; Bigam, C. G.; Holm, A.; Hodges, R. S.; Sykes, B. D. 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J. Biomol. NMR 1995, 5, 67. 44. Serrano, L. Comparison between the Phi Distribution of the Amino-Acids in the Protein Database and Nmr Data Indicates That Amino-Acids Have Various Phi Propensities in the Random Coil Conformation. J. Mol. Biol. 1995, 254, 322. 45. Baldwin, R. L.; Rose, G. D. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 1999, 24, 77. 46. Chakrabartty, A.; Baldwin, R. L. Stability of α-helices. Adv. Protein Chem. 1995, 46, 141. 47. Rose, G. D.; Gierasch, L. M.; Smith, J. A. Turns in peptides and proteins. Adv. Protein Chem. 1985, 37, 1. 48. Dyson, H. J.; Wright, P. E. Defining solution conformations of small linear peptides. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 519. 49. Blanco, F. J.; Jimenez, M. A.; Herranz, J.; Rico, M.; Santoro, J.; Nieto, J. L. NMR evidence of a short linear peptide that folds into a β-hairpin in aqueous-solution. J. Am. Chem. Soc. 1993, 115, 5887. 50. Blanco, F. J.; Rivas, G.; Serrano, L. A short linear peptide that folds into a native stable β-hairpin in aqueous-solution. Nat. Struct. Biol. 1994, 1, 584. 51. Gellman, S. H. Minimal model systems for β sheet secondary structure in proteins. Curr. Opin. Chem. Biol. 1998, 2, 717. 52. Stanger, H. E.; Gellman, S. H. Rules for antiparallel β-sheet design: D-Pro-Gly is superior to L-Asn-Gly for β-hairpin nucleation. J. Am. Chem. Soc. 1998, 120, 4236. 53. Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. De novo design and structural analysis of a model β-hairpin peptide system. Nat. Struct. Biol. 1996, 3, 604. 54. Searle, M. S.; Williams, D. H.; Packman, L. C. A short linear peptide derived from the N-terminal sequence of ubiquitin folds into a water-stable nonnative β-hairpin. Nat. Struct. Biol. 1995, 2, 999. 55. Maynard, A. J.; Sharman, G. J.; Searle, M. S. Origin of β-Hairpin Stability in Solution: Structural and Thermodynamic Analysis of the Folding of a Model Peptide Supports Hydrophobic Stabilization in Water. J. Am. Chem. Soc. 1998, 120, 1996. 56. Butterfield, S. M.; Waters, M. L. A designed β-hairpin peptide for molecular recognition of ATP in water. J. Am. Chem. Soc. 2003, 125, 9580. 57. Stewart, A. L.; Park, J. H.; Waters, M. L. Redesign of a WW domain peptide for selective recognition of single-stranded DNA. Biochemistry. 2011, 50, 2575. 58. Cline, L. L.; Waters, M. L. Design of a β-hairpin peptide-intercalator conjugate for simultaneous recognition of single stranded and double stranded regions of RNA. Org. Biomol. Chem. 2009, 7, 4622. 59. Imming, P.; Sinning, C.; Meyer, A. Opinion - Drugs, their targets and the nature and number of drug targets. Nat. Rev. Drug. Discov. 2006, 5, 821. 60. Wells, J. A.; McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450, 1001. 61. Fasan, R.; Dias, R. L. A.; Moehle, K.; Zerbe, O.; Vrijbloed, J. W.; Obrecht, D.; Robinson, J. A. Using a β-hairpin to mimic an α-helix: Cyclic peptidomimetic inhibitors of the p53-HDM2 protein-protein interaction. Angew. Chem. Int. Edit. 2004, 43, 2109. 62. Robinson, J. A.; DeMarco, S.; Gombert, F.; Moehle, K.; Obrecht, D. The design, structures and therapeutic potential of protein epitope mimetics. Drug Discov. Today 2008, 13, 944. 63. Horovitz, A.; Fersht, A. R. Strategy for Analyzing the cooperativity of intramolecular interactions in peptides and proteins. J. Mol. Biol. 1990, 214, 613. 64. Schreiber, G.; Fersht, A. R. Energetics of protein-protein interactions - analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mol. Biol. 1995, 248, 478. 65. Serrano, L.; Bycroft, M.; Fersht, A. R. Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. J. Mol. Biol. 1991, 218, 465. 66. Shi, Z. S.; Olson, C. A.; Kallenbach, N. R. Cation-pi interaction in model α-helical peptides. J. Am. Chem. Soc. 2002, 124, 3284. 85 67. Sharman, G. J.; Searle, M. S. Cooperative interaction between the three strands of a designed antiparallel β-sheet. J. Am. Chem. Soc. 1998, 120, 5291. 68. Blanco, F. J.; Serrano, L. Folding of Protein-G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure Elements. Eur. J. Biochem. 1995, 230, 634. 69. Tatko, C. D.; Waters, M. L. The geometry and efficacy of cation-pi interactions in a diagonal position of a designed β-hairpin. Protein Sci. 2003, 12, 2443. 70. Perutz, M. F. Electrostatic effects in proteins. Science 1978, 201, 1187. 71. Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133. 72. Thornton, J. M. Electrostatic interactions in proteins. Nature 1982, 295, 13. 73. Barlow, D. J.; Thornton, J. M. Ion-pairs in proteins. J. Mol. Biol. 1983, 168, 867. 74. Anderson, D. E.; Becktel, W. J.; Dahlquist, F. W. pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry 1990, 29, 2403. 75. Syud, F. A.; Stanger, H. E.; Gellman, S. H. Interstrand side chain-side chain interactions in a designed β-hairpin: Significance of both lateral and diagonal pairings. J. Am. Chem. Soc. 2001, 123, 8667. 76. Wilmot, C. M.; Thornton, J. M. Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 1988, 203, 221. 77. Atherton, E.; Fox, H.; Harkiss, D.; Logan, C. J.; Sheppard, R. C.; Williams, B. J. Mild procedure for solid-phase peptide-synthesis- Use of 'Fluorenylmethoxycarbonylamino- Acids. J. Chem. Soc. Chem. Comm. 1978, 537. 78. Fields, G. B.; Noble, R. L. Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. Int. J. Pept. Protein Res. 1990, 35, 161. 79. Volkmer-Engert, R.; Landgraf, C.; Schneider-Mergener, J. Charcoal surface-assisted catalysis of intramolecular disulfide bond formation in peptides. J. Pept. Res. 1998, 51, 365. 80. Bax, A.; Davis, D. G. Mlev-17-Based Two-Dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 1985, 65, 355. 81. Aue, W. P.; Bartholdi, E.; Ernst, R. R. Two-dimensional spectroscopy. Application to nuclear magnetic resonance. J. Chem. Phys. 1976, 64, 2229. 82. Bothnerby, A. A.; Stephens, R. L.; Lee, J. M.; Warren, C. D.; Jeanloz, R. W. Structure determination of a tetrasaccharide - Transient nuclear overhauser effects in the rotating frame. J. Am. Chem. Soc. 1984, 106, 811. 86 83. Jeener, J.; Meier, B. H.; Bachmann, P.; Ernst, R. R. Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys. 1979, 71, 4546. 84. Volkmer-Engert, R.; Landgraf, C.; Schneider-Mergener, J. Charcoal surface-assisted catalysis of intramolecular disulfide bond formation in peptides. J. Pept. Res. 1998, 51, 365. 85. Piotto, M.; Saudek, V.; Sklenar, V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 1992, 2, 661. 86. Kim, Y. M.; Prestegard, J. H. Measurement of Vicinal CoupCouplings from Cross Peaks in Cosy Spectra. J. Magn. Reson. 1989, 84, 9. Chapter3. 1. Crick, F. Central Dogma of Molecular Biology. Nature 1970, 227, 561. 2. Wu, G.; Morris, S. M., Jr. Arginine metabolism: nitric oxide and beyond. The Biochemical journal 1998, 336, 1. 3. Mitchell, D. J.; Kim, D. T.; Steinman, L.; Fathman, C. G.; Rothbard, J. B. Polyarginine enters cells more efficiently than other polycationic homopolymers. J. Pept. Res. 2000, 56, 318. 4. Pabo, C. O.; Sauer, R. T. Transcription factors - structural families and principles of DNA recognition. Annu. Rev. Biochem. 1992, 61, 1053. 5. Hope, I. A.; Struhl, K. Gcn4, a Eukaryotic Transcriptional activator protein, binds as a dimer to Target DNA. EMBO J. 1987, 6, 2781. 6. Struhl, K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem. Sci. 1989, 14, 137. 7. Landschulz, W. H.; Johnson, P. F.; Mcknight, S. L. The leucine zipper - a hypothetical structure common to a new class of DNA-binding proteins. Science 1988, 240, 1759. 8. Johnson, P. F.; Mcknight, S. L. Eukaryotic transcriptional regulatory proteins. Annu. Rev. Biochem. 1989, 58, 799. 9. Hope, I. A.; Struhl, K. GCN4, a eukaryotic transcriptional activator protein, binds as a dimer to target DNA. EMBO J. 1987, 6, 2781. 10. Keller, W.; Konig, P.; Richmond, T. J. Crystal-structure of a bZIP/DNA complex at 2.2 A - determinants of DNA specific recognition. J. Mol. Biol. 1995, 254, 657. 11. Sellers, J. W.; Vincent, A. C.; Struhl, K. Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol. Cell. Biol. 1990, 10, 5077. 12. Ellenberger, T. E.; Brandl, C. J.; Struhl, K.; Harrison, S. C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices - crystal-structure of the protein-DNA complex. Cell 1992, 71, 1223. 13. Joachimiak, A.; Haran, T. E.; Sigler, P. B. Mutagenesis supports water mediated recognition in the Trp repressor-operator system. EMBO J. 1994, 13, 367. 163 14. Montminy, M. R.; Bilezikjian, L. M. Binding of a nuclear-protein to the cyclic-AMP response element of the somatostatin gene. Nature 1987, 328, 175. 15. Peterson, B. R.; Sun, L. J.; Verdine, G. L. A critical arginine residue mediates cooperativity in the contact interface between transcription factors NFAT and AP-1. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 13671. 16. Chan, I. S.; Shahravan, S. H.; Fedorova, A. V.; Shin, J. A. The bZIP targets overlapping DNA subsites within a half-site, resulting in increased binding affinities. Biochemistry 2008, 47, 9646. 17. Buhrlage, S. J.; Bates, C. A.; Rowe, S. P.; Minter, A. R.; Brennan, B. B.; Majmudar, C. Y.; Wemmer, D. E.; Al-Hashimi, H.; Mapp, A. K. Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors. Acs. Chem. Biol. 2009, 4, 335. 18. Yao, S.; Brickner, M.; Pares-Matos, E. I.; Chmielewski, J. Uncoiling c-Jun coiled coils: Inhibitory effects of truncated fos peptides on jun dimerization and DNA binding in vitro. Biopolymers 1998, 47, 277. 19. Dervan, P. B.; Burli, R. W. Sequence-specific DNA recognition by polyamides. Curr. Opin. Chem. Biol. 1999, 3, 688. 20. Mapp, A. K.; Ansari, A. Z.; Ptashne, M.; Dervan, P. B. Activation of gene expression by small molecule transcription factors. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 3930. 21. Talanian, R. V.; Mcknight, C. J.; Rutkowski, R.; Kim, P. S. Minimum Length of a Sequence-Specific DNA-Binding Peptide. Biochemistry 1992, 31, 6871. 22. Talanian, R. V.; Mcknight, C. J.; Kim, P. S. Sequence-specific DNA-binding by a short peptide dimer. Science 1990, 249, 769. 23. Talanian, R. V.; Mcknight, C. J.; Rutkowski, R.; Kim, P. S. Minimum length of a sequence-specific DNA-binding peptide. Biochemistry 1993, 32, 1688. 24. Neuberg, M.; Schuermann, M.; Hunter, J. B.; Muller, R. Two functionally different regions in Fos are required for the sequence-specific DNA interaction of the Fos Jun Protein complex. Nature 1989, 338, 589. 25. Oneil, K. T.; Hoess, R. H.; Degrado, W. F. Design of DNA-binding peptides based on the leucine zipper motif. Science 1990, 249, 774. 26. Lajmi, A. R.; Lovrencic, M. E.; Wallace, T. R.; Thomlinson, R. R.; Shin, J. A. Minimalist, alanine-based, helical protein dimers bind to specific DNA sites. J. Am. Chem. Soc. 2000, 122, 5638. 164 27. Edelhoch, H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 1967, 6, 1948. 28. Pace, C. N.; Vajdos, F.; Fee, L.; Grimsley, G.; Gray, T. How to measure and predict the molar absorption-coefficient of a protein. Protein Sci. 1995, 4, 2411. 29. Volkmer-Engert, R.; Landgraf, C.; Schneider-Mergener, J. Charcoal surface-assisted catalysis of intramolecular disulfide bond formation in peptides. J. Pept. Res. 1998, 51, 365. 30. Johnson, W. C. Protein Secondary structure and circular-dichroism - a practical guide. Proteins Struc. Func. and Genet. 1990, 7, 205. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/64682 | - |
dc.description.abstract | 摺板結構為其中一個主要的蛋白質二級結構,主要由strand
間藉由許多穩定的作用力所形成。因此,探討摺板結構的穩定性有助於了解蛋白質的結構。髮夾結構是最常用來探討摺板結構的模型,因為其為最簡單的摺板結構,由兩條β-strand所構成。然而在許多的作用力之中,帶電荷胺基酸彼此之間的靜電作用力,對整 個構形的穩定度有很大的貢獻。在自然界裡面帶電荷的胺基酸,其側鏈長短都有 所不一,因此我們藉由髮夾結構去探討帶電荷胺基酸的側鏈長短,對於兩條strand 之間,正負吸引力的影響以及對於整個髮夾結構的影響。根據2D-NMR 實驗的實 驗顯示,具有較長側鏈的胺基酸可以提供較好正負電荷之間的吸引力還有較高的 結構穩定性。由於正負電荷之間的吸引力不只對蛋白質本身結構的穩定性很重要, 對於辨識DNA 也扮演很重要的角色。因此,我們用真核生物轉錄活化蛋白質GCN4 其上面基本區域(basicregion)的精氨酸側鏈電荷來探討GCN4 上個別精氨酸對於CRE DNA 還有AP-1 DNA 辨識能力的影響•.本研究利用瓜氨酸取代精氨酸來探討電荷對於結合能力及選擇性影響,並且利用電泳技術分析合成之胜肽對於特定DNA 之間作用關係•.本研究顯示WtArgGCN4ss和MinArg11Ass以及MinArg4Ass作為對照組與其不同實驗組對照發現,WtArgGCN4ss 實驗組顯示相對 MinArg11Ass較高的結合能力•.除外,WtCit18GCN4ss表現出相對於對照組以及其他實驗組較差的專一性;WtGCN4Cit24ss 擁有比WtArgGCN4ss 更好的專一性 Min11ACit2ss 表現出相對於對照組(MinArg11Ass)以及其他實驗組較好的專一性•. 本研究利用理論計算的方式模擬合成出的實驗組胜肽與DNA之間的結合情形。 | zh_TW |
dc.description.abstract | β-Sheet is a very common secondary structure in proteins. A β-sheet consists of twoor more β-strands linked and stabilized by hydrogen bonds between adjacent strands.Moreover, ion pairing interactions between β-strands can stabilize the β-sheetconformation. Interestingly, the natural charged amino acids, which form ion pairs, havedifferent side chain lengths. To investigate how the side chain length affects stability,β-hairpin was used as a model system, because β-hairpins represent the simplest form ofantiparallel β-sheets. Three lateral cross strand ion pairs were investigated: Aad-Orn,
Glu-Orn, and Aad-Lys. Peptides with different glutamate and lysine analogs were synthesized by solid phase peptide synthesis using Fmoc-based chemistry: HPTAadOrn,HPTAadLys, and HPTGluOrn, and all purified to at least 95% purity. We alsosynthesized fully folded peptides and unfolded peptides as references. The structure ofthe fraction folded of β-hairpin were analyzed based on the NMR TOCSY, DQF-COSY,NOESY, and ROESY spectra. After assigning the chemical shifts, the secondarystructure of the peptides were confirmed. The folding percentage followed the trend HPTAadLys ≥HPTAadOrn > HPTGluOrn. There was no significant difference between peptides with different lysine analogs. However, the longer side chain gave higherstability for the peptides with different glutamate analogs. This trend revealed that properside chain length of charged residues could promote of β-hairpin formation. Interestingly,the lateral cross strand interaction followed the trend: Aad-Lys > Aad-Orn > Glu-Orn.These two trends are apparently complimentary to one another. The residues with longerside chain length contribute more to the interaction to favor β-hairpin formation. Arg-bearing proteins play important roles in DNA recognition. To study how thearginine side chain charge affects DNA recognition, peptides derived from the GCN4basic region with each individual arginine replaced with a neutral amino acid citrulline(Cit) were investigated. These peptides were synthesized by solid phase peptidesynthesis using Fmoc-based chemistry. Gel shift assays were used to determine thebinding affinity and specificity of the peptides with activator proein-1 (AP-1). TheWtArgGCN4ss mutants showed higher affinity and specificity compared to theMinArg11Ass and MinArg4Ass mutants. WtGCN4Cit24ss showed higher affinity andspecificity compared to WtArgGCN4ss. Molecular mechanic calculations wereperformed to explain the gel shift results. CD spectroscopy indicated that all ourinvestigated peptides remained somewhat helical. The positive charge on Arg243 is very important for binding DNA, mutating other ariginines can modulate and even increase the binding affinity. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T22:57:21Z (GMT). No. of bitstreams: 1 ntu-101-R99223213-1.pdf: 13691806 bytes, checksum: 8c0e300511bcaf49b33816f63eab8f6a (MD5) Previous issue date: 2012 | en |
dc.description.tableofcontents | 口試口委會審定書.........................................................I
誌謝............................................................................................................... II 中文摘要 ................................................................... III Abstract .............................................................................................. IV Table of Contents ................................................................................... VII List of Figures ..................................................................................... X List of Tables ...................................................................... XIII Abbreviations .................................................................. XV Chapter 1 ........................................................................... 1 Introduction ...................................................................................... 1 Central Dogma of Molecular Biology....................2 Protein Structure.............................................3 Driving ForceforProteinFolding .........................................10 Hyperthermophilic Proteins and Electrostatic Interactions.......12 Thesis Overview ......................................................................... 14 Reference ................................................................ 15 Chapter 2 The Effect of Side Chain Length on the Cross-StrandIon Pairing Interactions in β-Hairpins ................................................................................................................ 19 Introduction .................................................................................. 20 β-Sheets.........................................20 β-Sheet Propensity..............................................................................22 Cross-Strand Interactions................................................23 β-Turns...........................25 β-Turn Propensity ...................................................................................................26 β-Hairpins..........................................................................28 β-Hairpin as a Model System...........................................30 Well-Defined Model System..................................................31 β-Hairpin Applications..................................32 Double-Mutant Cycle..............................................................33 Different Side Chain Lengths of Charged Amino Acids...............35 Chapter Overview ................................................................. 36 Results and Discussion ....................................................... 37 Peptide Design.........................................37 Peptide Synthesis and Purification...............................................39 NMR Spectroscopy................................................................40 Characterization of the β-Hairpin Structure.......................................41 Conclusions ................................................................ 63 Acknowledgements ................................................................ 64 Experimental Section ........................................................................ 65 General Materials and Methods..........................................................65 Solid Phase Peptide Synthesis and Purification....................66 Charcoal Mediated Intramolecular Disulfide Formation....................68 References ................................................................................ 80 Αppendix A. ....................................................................................... 87 Chapter 3 The Effect of Arginine Side Chain Charge on DNA Recognition by GCN4-Derived Peptides. ....................................................................... 96 Introduction .................................................................... 97 DNA......................................................................97 GCN4.....................................................................................................99 Artificial Transcription Factors (ATF)............................................102 GCN4 Based DNA Binding ATF........................................................103 Chapter Overview...........................................................104 Results and Discussion ........................................................ 105 Peptide Design..................................................105 Peptide Synthesis and Purification..................................107 Circular Dichroism Spectroscopy..............................................138 Modeling of Peptides-DNA Complexes by Molecular Mechanics Calculations 139 Conclusion .................................................................................... 142 Acknowledgements ................................................................................ 143 Experimental Section .................................................................. 144 General Materials and Methods..........................................................144 Solid Phase Peptide Synthesis............................................................146 Charcoal Mediated Intermolecular Disulfide Formation...........................148 UV-Visible Spectroscopy (UV-vis)........158 Gel Shift Assay..............................................................158 Modeling by Molecular Mechanics Calculations....................................159 References ........................................ 162 | |
dc.language.iso | zh-TW | |
dc.title | 正負電荷側鏈長度對β-hairpin 的影響及精胺酸側鏈電荷對辨認DNA 的影響 | zh_TW |
dc.title | The Effect of Side Chain Length on the Cross-Strand Ion Pairing Interactions in β-Hairpins and Arginine Side Chain Charge on DNA Recognition | en |
dc.type | Thesis | |
dc.date.schoolyear | 100-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 黃人則,陳佩燁 | |
dc.subject.keyword | 摺板結構,髮夾結構,正負電荷作用力,DNA 辨認, | zh_TW |
dc.subject.keyword | β-sheet,β-hairpin,electrostatic interaction,DNA recognition, | en |
dc.relation.page | 164 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2012-08-09 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 化學研究所 | zh_TW |
顯示於系所單位: | 化學系 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-101-1.pdf 目前未授權公開取用 | 13.37 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。