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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 陳平 | |
dc.contributor.author | Hao-Chun Hsu | en |
dc.contributor.author | 許皓鈞 | zh_TW |
dc.date.accessioned | 2021-06-13T05:45:00Z | - |
dc.date.available | 2016-08-04 | |
dc.date.copyright | 2011-08-04 | |
dc.date.issued | 2011 | |
dc.date.submitted | 2011-07-26 | |
dc.identifier.citation | 1. Gavin, A. C.; Aloy, P.; Grandi, P.; Krause, R.; Boesche, M.; Marzioch, M.; Rau, C.; Jensen, L. J.; Bastuck, S.; Dumpelfeld, B.; Edelmann, A.; Heurtier, M. A.; Hoffman, V.; Hoefert, C.; Klein, K.; Hudak, M.; Michon, A. M.; Schelder, M.; Schirle, M.; Remor, M.; Rudi, T.; Hooper, S.; Bauer, A.; Bouwmeester, T.; Casari, G.; Drewes, G.; Neubauer, G.; Rick, J. M.; Kuster, B.; Bork, P.; Russell, R. B.; Superti-Furga, G. Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440, 631-636.
2. Hall, A. Rho GTPases and the actin cytoskeleton. Science 1998, 279, 509-514. 3. Bairoch, A. The ENZYME database in 2000. Nucleic Acids Res. 2000, 28, 304-305. 4. Bolon, D. N.; Mayo, S. L. Enzyme-like proteins by computational design. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 14274-14279. 5. Radzicka, A.; Wolfenden, R. A proficient enzyme. Science 1995, 267, 90-93. 6. Prusiner, S. B. Molecular-biology of prion diseases. Science 1991, 252, 1515-1522. 7. Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. O.; Riekel, C.; Grothe, R.; Eisenberg, D. Structure of the cross-β spine of amyloid-like fibrils. Nature 2005, 435, 773-778. 8. Talanian, R. V.; Mcknight, C. J.; Kim, P. S. Sequence-specific DNA-binding by a short peptide dimer. Science 1990, 249, 769-771. 9. Pavletich, N. P.; Pabo, C. O. Zinc finger DNA recognition - crystal-structure of a Zif268-DNA complex at 2.1-A. Science 1991, 252, 809-817. 10. Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133-7155. 11. Elcock, A. H. The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins. J. Mol. Biol. 1998, 284, 489-502. 12. Scholtz, J. M.; Qian, H.; Robbins, V. H.; Baldwin, R. L. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry 1993, 32, 9668-9676. 13. Thomas, A. S.; Elcock, A. H. Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures. J. Am. Chem. Soc. 2004, 126, 2208-2214. 14. Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 1999, 289, 1435-1444. 15. Baldwin, R. L.; Rose, G. D. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 1999, 24, 26-33. 16. Baldwin, R. L.; Rose, G. D. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 1999, 24, 77-83. 17. 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, 211-222. 18. Kabsch, W.; Sander, C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637. 19. Barlow, D. J.; Thornton, J. M. Ion-pairs in proteins. J. Mol. Biol. 1983, 168, 867-885. 20. Cheng, R. P.; Girinath, P.; Ahmad, R. Effect of lysine side chain length on intra-helical glutamate-lysine ion pairing interactions. Biochemistry 2007, 46, 10528-10537. 21. Cheng, R. P.; Girinath, P.; Suzuki, Y.; Kuo, H. T.; Hsu, H. C.; Wang, W. R.; Yang, P. A.; Gullickson, D.; Wu, C. H.; Koyack, M. J.; Chiu, H. P.; Weng, Y. J.; Hart, P.; Kokona, B.; Fairman, R.; Lin, T. E.; Barrett, O. Positional effects on helical Ala-based peptides. Biochemistry 2010, 49, 9372-9384. 22. Barlow, D. J.; Thornton, J. M. Helix geometry in proteins. J. Mol. Biol. 1988, 201, 601-619. 23. Doig, A. J.; Andrew, C. D.; Cochran, D. A. E.; Hughes, E.; Penel, S.; Sun, J. K.; Stapley, B. J.; Clarke, D. T.; Jones, G. R. Structure, stability and folding of the α-helix. From Protein Folding to New Enzymes 2001, 95-110. 24. Hussain, F. Pauling and a helix. Trends Biochem. Sci. 1976, 1, N37-N38. 25. Edsall, J. T.; Flory, P. J.; Kendrew, J. C.; Liquori, A. M.; Nemethy, G.; Ramachandran, G. N.; Scheraga, H. A. A proposal of standard conventions and nomenclature for description of polypeptide conformations. J. Mol. Biol. 1966, 15, 399-407. 26. Lifson, S. Theory of helix-coil transition in polypeptides. J. Chem. Phys. 1961, 34, 1963-1974. 27. Rohl, C. A.; Scholtz, J. M.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Kinetics of amide proton-exchange in helical peptides of varying chain lengths - Interpretation by the Lifson-Roig equation. Biochemistry 1992, 31, 1263-1269. 28. 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, 205-211. 29. Richardson, J. S.; Richardson, D. C. Amino-acid preferences for specific locations at the ends of α-helices. Science 1988, 240, 1648-1652. 30. Karpen, M. E.; Dehaseth, P. L.; Neet, K. E. Differences in the amino-acid distributions of 310-helices and α-helices. Protein Sci. 1992, 1, 1333-1342. 31. Chakrabartty, A.; Doig, A. J.; Baldwin, R. L. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 11332-11336. 32. Doig, A. J.; Baldwin, R. L. N- and C-Capping preferences for all 20 amino-acids in α-helical peptides. Protein Sci. 1995, 4, 1325-1336. 33. Rohl, C. A.; Chakrabartty, A.; Baldwin, R. L. Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol. Protein Sci. 1996, 5, 2623-2637. 34. Doig, A. J.; Chakrabartty, A.; Klingler, T. M.; Baldwin, R. L. Determination of free-energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N-Capping and C-Capping. Biochemistry 1994, 33, 3396-3403. 35. Zimm, B. H.; Bragg, J. K. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 1959, 31, 526-535. 36. Merutka, G.; Stellwagen, E. Positional independence and additivity of amino acid replacements on helix stability in monomeric peptides. Biochemistry 1990, 29, 894-898. 37. Ermolenko, D. N.; Richardson, J. M.; Makhatadze, G. I. Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the α-helix have the same helical propensity. Protein Sci. 2003, 12, 1169-1176. 38. Petukhov, M.; Munoz, V.; Yumoto, N.; Yoshikawa, S.; Serrano, L. Position dependence of non-polar amino acid intrinsic helical propensities. J. Mol. Biol. 1998, 278, 279-289. 39. Petukhov, M.; Uegaki, K.; Yumoto, N.; Yoshikawa, S.; Serrano, L. Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln. Protein Sci. 1999, 8, 2144-2150. 40. Petukhov, M.; Uegaki, K.; Yumoto, N.; Serrano, L. Amino acid intrinsic α-helical propensities III: Positional dependence at several positions of C terminus. Protein Sci. 2002, 11, 766-777. 41. Job, G. E.; Kennedy, R. J.; Heitmann, B.; Miller, J. S.; Walker, S. M.; Kemp, D. S. Temperature- and length-dependent energetics of formation for polyalanine helices in water: Assignment of w(Ala)(n,T) and temperature-dependent CD ellipticity standards. J. Am. Chem. Soc. 2006, 128, 8227-8233. 42. Kennedy, R. J.; Tsang, K. Y.; Kemp, D. S. Consistent helicities from CD and template t/c data for N-templated polyalanines: Progress toward resolution of the alanine helicity problem. J. Am. Chem. Soc. 2002, 124, 934-944. 43. Padmanabhan, S.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Helix propensities of basic amino acids increase with the length of the side-chain. J. Mol. Biol. 1996, 257, 726-734. 44. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994, 3, 843-852. 45. Padmanabhan, S.; Baldwin, R. L. Straight-chain nonpolar amino-acids are good helix-formers in water. J. Mol. Biol. 1991, 219, 135-137. 46. Andrew, C. D.; Penel, S.; Jones, G. R.; Doig, A. J. Stabilizing nonpolar/polar side-chain interactions in the α-helix. Proteins: Struct., Funct., Genet. 2001, 45, 449-455. 47. Hill, R. B.; Raleigh, D. P.; Lombardi, A.; Degrado, W. F. De novo design of helical bundles as models for understanding protein folding and function. Acc. Chem. Res. 2000, 33, 745-754. 48. Marqusee, S.; Baldwin, R. L. Helix stabilization by Glu- ... Lys+ salt bridges in short peptides of denovo design. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 8898-8902. 49. Huyghuesdespointes, B. M. P.; Scholtz, J. M.; Baldwin, R. L. Helical peptides with 3 pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci. 1993, 2, 80-85. 50. Fields, G. B.; Noble, R. L. Solid-phase peptide-synthesis utilizing 9-fluorenylmethoxycarbonyl amino-acids. Int. J. Pept. Protein Res. 1990, 35, 161-214. 51. Padmanabhan, S.; Marqusee, S.; Ridgeway, T.; Laue, T. M.; Baldwin, R. L. Relative helix-forming tendencies of nonpolar amino-acids. Nature 1990, 344, 268-270. 52. Marqusee, S.; Baldwin, R. L. The role of intrahelical ion-pairs in α-helix formation by synthetic peptides. J. Cell. Biochem. 1987, 227-227. 53. Armstrong, K. M.; Fairman, R.; Baldwin, R. L. The (i, i+4) Phe-His interaction studied in an alanine-based α-helix. J. Mol. Biol. 1993, 230, 284-291. 54. Klingler, T. M.; Brutlag, D. L. Discovering structural correlations in α-helices. Protein Sci. 1994, 3, 1847-1857. 55. Shi, Z. S.; Olson, C. A.; Bell, A. J.; Kallenbach, N. R. Stabilization of α-helix structure by polar side-chain interactions: Complex salt bridges, cation-π interactions, and C-H ... O H-bonds. Biopolymers 2001, 60, 366-380. 56. Doig, A. J. Recent advances in helix-coil theory. Biophys. Chem. 2002, 101, 281-293. 57. Robert, C. H. A hierarchical nesting approach to describe the stability of α-helices with side-chain interactions. Biopolymers 1990, 30, 335-347. 1. 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, 211-222. 2. Kabsch, W.; Sander, C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637. 3. Barlow, D. J.; Thornton, J. M. Ion-pairs in proteins. J. Mol. Biol. 1983, 168, 867-885. 4. Cheng, R. P.; Girinath, P.; Ahmad, R. Effect of lysine side chain length on intra-helical glutamate-lysine ion pairing interactions. Biochemistry 2007, 46, 10528-10537. 5. Cheng, R. P.; Girinath, P.; Suzuki, Y.; Kuo, H. T.; Hsu, H. C.; Wang, W. R.; Yang, P. A.; Gullickson, D.; Wu, C. H.; Koyack, M. J.; Chiu, H. P.; Weng, Y. J.; Hart, P.; Kokona, B.; Fairman, R.; Lin, T. E.; Barrett, O. Positional effects on helical Ala-based peptides. Biochemistry 2010, 49, 9372-9384. 6. Barlow, D. J.; Thornton, J. M. Helix geometry in proteins. J. Mol. Biol. 1988, 201, 601-619. 7. Cheng, R. P. Beyond de novo protein design - de novo design of non-natural folded oligomers. Curr. Opin. Struct. Biol. 2004, 14, 512-520. 8. Gellman, S. H. Foldamers: A manifesto. Acc. Chem. Res. 1998, 31, 173-180. 9. Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. A field guide to foldamers. Chem. Rev. 2001, 101, 3893-4011. 10. Sanford, A. R.; Gong, B. Evolution of helical foldamers. Curr. Org. Chem. 2003, 7, 1649-1659. 11. Lifson, S. Theory of helix-coil transition in polypeptides. J. Chem. Phys. 1961, 34, 1963-1974. 12. Zimm, B. H.; Bragg, J. K. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 1959, 31, 526-535. 13. Merutka, G.; Stellwagen, E. Positional independence and additivity of amino acid replacements on helix stability in monomeric peptides. Biochemistry 1990, 29, 894-898. 14. Ermolenko, D. N.; Richardson, J. M.; Makhatadze, G. I. Noncharged amino acid residues at the solvent-exposed positions in the middle and at the C terminus of the α-helix have the same helical propensity. Protein Sci. 2003, 12, 1169-1176. 15. Petukhov, M.; Munoz, V.; Yumoto, N.; Yoshikawa, S.; Serrano, L. Position dependence of non-polar amino acid intrinsic helical propensities. J. Mol. Biol. 1998, 278, 279-289. 16. Petukhov, M.; Uegaki, K.; Yumoto, N.; Yoshikawa, S.; Serrano, L. Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln. Protein Sci. 1999, 8, 2144-2150. 17. Petukhov, M.; Uegaki, K.; Yumoto, N.; Serrano, L. Amino acid intrinsic α-helical propensities III: Positional dependence at several positions of C terminus. Protein Sci. 2002, 11, 766-777. 18. Job, G. E.; Kennedy, R. J.; Heitmann, B.; Miller, J. S.; Walker, S. M.; Kemp, D. S. Temperature- and length-dependent energetics of formation for polyalanine helices in water: Assignment of w(Ala)(n,T) and temperature-dependent CD ellipticity standards. J. Am. Chem. Soc. 2006, 128, 8227-8233. 19. Kennedy, R. J.; Tsang, K. Y.; Kemp, D. S. Consistent helicities from CD and template t/c data for N-templated polyalanines: Progress toward resolution of the alanine helicity problem. J. Am. Chem. Soc. 2002, 124, 934-944. 20. Andrew, C. D.; Penel, S.; Jones, G. R.; Doig, A. J. Stabilizing nonpolar/polar side-chain interactions in the α-helix. Proteins: Struct., Funct., Genet. 2001, 45, 449-455. 21. Chakrabartty, A.; Doig, A. J.; Baldwin, R. L. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. U. S. A. 1993, 90, 11332-11336. 22. Rohl, C. A.; Chakrabartty, A.; Baldwin, R. L. Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol. Protein Sci. 1996, 5, 2623-2637. 23. Hill, R. B.; Raleigh, D. P.; Lombardi, A.; Degrado, W. F. De novo design of helical bundles as models for understanding protein folding and function. Acc. Chem. Res. 2000, 33, 745-754. 24. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994, 3, 843-852. 25. Padmanabhan, S.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Helix propensities of basic amino acids increase with the length of the side-chain. J. Mol. Biol. 1996, 257, 726-734. 26. Marqusee, S.; Baldwin, R. L. Helix stabilization by Glu- ... Lys+ salt bridges in short peptides of denovo design. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 8898-8902. 27. Huyghuesdespointes, B. M. P.; Scholtz, J. M.; Baldwin, R. L. Helical peptides with 3 pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci. 1993, 2, 80-85. 28. Fields, G. B.; Noble, R. L. Solid-phase peptide-synthesis utilizing 9-fluorenylmethoxycarbonyl amino-acids. Int. J. Pept. Protein Res. 1990, 35, 161-214. 29. Padmanabhan, S.; Marqusee, S.; Ridgeway, T.; Laue, T. M.; Baldwin, R. L. Relative helix-forming tendencies of nonpolar amino-acids. Nature 1990, 344, 268-270. 30. Doig, A. J.; Baldwin, R. L. N- and C-Capping preferences for all 20 amino-acids in α-helical peptides. Protein Sci. 1995, 4, 1325-1336. 31. Aurora, R.; Rose, G. D. Helix capping. Protein Sci. 1998, 7, 21-38. 32. Richardson, J. S.; Richardson, D. C. Amino-acid preferences for specific locations at the ends of α-helices. Science 1988, 240, 1648-1652. 33. Dasgupta, S.; Bell, J. A. Design of helix ends. Amino acid preferences, hydrogen-bonding and electrostatic interactions. Int. J. Pept. Protein Res. 1993, 41, 499-511. 34. Kumar, S.; Bansal, M. Dissecting α-helices: Position-specific analysis of α-helices in globular proteins. Proteins: Struct., Funct., Genet. 1998, 31, 460-476.s 35. Baker, E. N.; Hubbard, R. E. Hydrogen-bonding in globular-proteins. Prog. Biophys. Mol. Biol. 1984, 44, 97-179. 36. Bolin, K. A.; Millhauser, G. L. a and 310: The split personality of polypeptide helices. Acc. Chem. Res. 1999, 32, 1027-1033. 37. Fiori, W. R.; Miick, S. M.; Millhauser, G. L. Increasing sequence length favors α-helix over 310-helix in alanine-based peptides - evidence for a length-dependent structural transition. Biochemistry 1993, 32, 11957-11962. 38. Miick, S. M.; Martinez, G. V.; Fiori, W. R.; Todd, A. P.; Millhauser, G. L. Short alanine-based peptides may form 310-helices and not α-helices in aqueous-solution. Nature 1992, 359, 653-655. 39. Munoz, V.; Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. Nat. Struct. Biol. 1994, 1, 399-409. 40. Bell, J. A.; Becktel, W. J.; Sauer, U.; Baase, W. A.; Matthews, B. W. Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of 6 amino-acid substitutions at Thr 59. Biochemistry 1992, 31, 3590-3596. 41. Lyulin, A. V.; Michels, M. A. J. Molecular dynamics simulation of bulk atactic polystyrene in the vicinity of Tg. Macromolecules 2002, 35, 1463-1472. 42. Eslami, H.; Muller-Plathe, F. Structure and Mobility of Poly(ethylene terephthalate): A Molecular Dynamics Simulation Study. Macromolecules 2009, 42, 8241-8250. 1. Rose, W. C. The nutritive significance of the amino acids and certain related compounds. Science 1937, 86, 298-300. 2. Beaumier, L.; Castillo, L.; Ajami, A. M.; Young, V. R. Urea cycle intermediate kinetics and nitrate excretion at normal and therapeutic intakes of arginine in humans. Am. J. Physiol. 1995, 269, E884-E896. 3. Tapiero, H.; Mathe, G.; Couvreur, P.; Tew, K. D. Dossier: Free amino acids in human health and pathologies - I. Arginine. Biomed. Pharmacother. 2002, 56, 439-445. 4. Diederich, F.; Hirsch, A. K. H.; Fischer, F. R. Phosphate recognition in structural biology. Angew. Chem. Int. Ed. 2007, 46, 338-352. 5. Uhrin, D.; Blaum, B. S.; Deakin, J. A.; Johansson, C. M.; Herbert, A. P.; Barlow, P. N.; Lyon, M. Lysine and arginine side chains in glycosaminoglycan-protein complexes investigated by NMR, cross-linking, and mass spectrometry: A case study of the factor H-heparin interaction. J. Am. Chem. Soc. 2010, 132, 6374-6381. 6. 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, 318-325. 7. 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, 211-222. 8. Kabsch, W.; Sander, C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637. 9. Barlow, D. J.; Thornton, J. M. Ion-pairs in proteins. J. Mol. Biol. 1983, 168, 867-885. 10. Cheng, R. P.; Girinath, P.; Ahmad, R. Effect of lysine side chain length on intra-helical glutamate-lysine ion pairing interactions. Biochemistry 2007, 46, 10528-10537. 11. Cheng, R. P.; Girinath, P.; Suzuki, Y.; Kuo, H. T.; Hsu, H. C.; Wang, W. R.; Yang, P. A.; Gullickson, D.; Wu, C. H.; Koyack, M. J.; Chiu, H. P.; Weng, Y. J.; Hart, P.; Kokona, B.; Fairman, R.; Lin, T. E.; Barrett, O. Positional effects on helical Ala-based peptides. Biochemistry 2010, 49, 9372-9384. 12. Barlow, D. J.; Thornton, J. M. Helix geometry in proteins. J. Mol. Biol. 1988, 201, 601-619. 13. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994, 3, 843-852. 14. Kemp, D. S.; Boyd, J. G.; Muendel, C. C. The helical s-constant for alanine in water derived from template-nucleated helices. Nature 1991, 352, 451-454. 15. Munoz, V.; Serrano, L. Elucidating the folding problem of helical peptides using empirical parameters. Nat. Struct. Biol. 1994, 1, 399-409. 16. Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133-7155. 17. Makhatadze, G. I.; Privalov, P. L. Energetics of protein structure. Adv. Protein Chem. 1995, 47, 307-425. 18. Padmanabhan, S.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Helix propensities of basic amino acids increase with the length of the side-chain. J. Mol. Biol. 1996, 257, 726-734. 19. Padmanabhan, S.; Baldwin, R. L. Straight-chain nonpolar amino-acids are good helix-formers in water. J. Mol. Biol. 1991, 219, 135-137. 20. Gupta, S.; Cheng, H.; Mollah, A. K. M. M.; Jamison, E.; Morris, S.; Chance, M. R.; Khrapunov, S.; Brenowitz, M. DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein. Biochemistry 2007, 46, 9886-9898. 21. Johnson, W. C. Protein secondary structure and circular-dichroism - a practical guide. Proteins: Struct., Funct., Genet. 1990, 7, 205-214. 22. Doig, A. J.; Baldwin, R. L. N- and C-Capping preferences for all 20 amino-acids in α-helical peptides. Protein Sci. 1995, 4, 1325-1336. 23. Edelhoch, H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 1967, 6, 1948-1954. 24. 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, 2411-2423. 25. Chakrabartty, A.; Kortemme, T.; Padmanabhan, S.; Baldwin, R. L. Aromatic side-chain contribution to far-ultraviolet circular-dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry 1993, 32, 5560-5565. 26. Fields, G. B.; Noble, R. L. Solid-phase peptide-synthesis utilizing 9-fluorenylmethoxycarbonyl amino-acids. Int. J. Pept. Protein Res. 1990, 35, 161-214. 27. Feichtinger, K.; Zapf, C.; Sings, H. L.; Goodman, M. Diprotected triflylguanidines: A new class of guanidinylation reagents. J. Org. Chem. 1998, 63, 3804-3805. 28. Feichtinger, K.; Sings, H. L.; Baker, T. J.; Matthews, K.; Goodman, M. Triurethane-protected guanidines and triflyldiurethane-protected guanidines: New reagents for guanidinylation reactions. J. Org. Chem. 1998, 63, 8432-8439. 29. Blagdon, D. E.; Goodman, M. Mechanisms of protein and polypeptide helix initiation. Biopolymers 1975, 14, 241-245. 30. Sali, D.; Bycroft, M.; Fersht, A. R. Stabilization of protein-structure by interaction of α-helix dipole with a charged side-chain. Nature 1988, 335, 740-743. 1. Klingler, T. M.; Brutlag, D. L. Discovering structural correlations in α-helices. Protein Sci. 1994, 3, 1847-1857. 2. Maxfield, F. R.; Scheraga, H. A. Effect of neighboring charges on helix forming ability of charged amino-acids in proteins. Macromolecules 1975, 8, 491-493. 3. Barlow, D. J.; Thornton, J. M. Ion-pairs in proteins. J. Mol. Biol. 1983, 168, 867-885. 4. Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133-7155. 5. Makhatadze, G. I.; Privalov, P. L. Energetics of protein structure. Adv. Protein Chem. 1995, 47, 307-425. 6. Elcock, A. H. The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins. J. Mol. Biol. 1998, 284, 489-502. 7. Thomas, A. S.; Elcock, A. H. Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures. J. Am. Chem. Soc. 2004, 126, 2208-2214. 8. Scholtz, J. M.; Qian, H.; Robbins, V. H.; Baldwin, R. L. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry 1993, 32, 9668-9676. 9. Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 1999, 289, 1435-1444. 10. 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, 211-222. 11. Kabsch, W.; Sander, C. Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637. 12. Cheng, R. P.; Girinath, P.; Ahmad, R. Effect of lysine side chain length on intra-helical glutamate-lysine ion pairing interactions. Biochemistry 2007, 46, 10528-10537. 13. Cheng, R. P.; Girinath, P.; Suzuki, Y.; Kuo, H. T.; Hsu, H. C.; Wang, W. R.; Yang, P. A.; Gullickson, D.; Wu, C. H.; Koyack, M. J.; Chiu, H. P.; Weng, Y. J.; Hart, P.; Kokona, B.; Fairman, R.; Lin, T. E.; Barrett, O. Positional effects on helical Ala-based peptides. Biochemistry 2010, 49, 9372-9384. 14. Barlow, D. J.; Thornton, J. M. Helix geometry in proteins. J. Mol. Biol. 1988, 201, 601-619. 15. Marqusee, S.; Baldwin, R. L. Helix stabilization by Glu- ... Lys+ salt bridges in short peptides of denovo design. Proc. Natl. Acad. Sci. U. S. A. 1987, 84, 8898-8902. 16. Edelhoch, H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 1967, 6, 1948-1954. 17. 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, 2411-2423. 18. Chakrabartty, A.; Kortemme, T.; Padmanabhan, S.; Baldwin, R. L. Aromatic side-chain contribution to far-ultraviolet circular-dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry 1993, 32, 5560-5565. 19. Feichtinger, K.; Sings, H. L.; Baker, T. J.; Matthews, K.; Goodman, M. Triurethane-protected guanidines and triflyldiurethane-protected guanidines: New reagents for guanidinylation reactions. J. Org. Chem. 1998, 63, 8432-8439. 20. Feichtinger, K.; Zapf, C.; Sings, H. L.; Goodman, M. Diprotected triflylguanidines: A new class of guanidinylation reagents. J. Org. Chem. 1998, 63, 3804-3805. 21. Fields, G. B.; Noble, R. L. Solid-phase peptide-synthesis utilizing 9-fluorenylmethoxycarbonyl amino-acids. Int. J. Pept. Protein Res. 1990, 35, 161-214. 22. Gupta, S.; Cheng, H.; Mollah, A. K. M. M.; Jamison, E.; Morris, S.; Chance, M. R.; Khrapunov, S.; Brenowitz, M. DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein. Biochemistry 2007, 46, 9886-9898. 23. Huyghuesdespointes, B. M. P.; Scholtz, J. M.; Baldwin, R. L. Helical peptides with 3 pairs of Asp-Arg and Glu-Arg residues in different orientations and spacings. Protein Sci. 1993, 2, 80-85. 24. Chakrabartty, A.; Kortemme, T.; Baldwin, R. L. Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 1994, 3, 843-852. 25. Doig, A. J.; Baldwin, R. L. N- and C-Capping preferences for all 20 amino-acids in α-helical peptides. Protein Sci. 1995, 4, 1325-1336. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/33718 | - |
dc.description.abstract | 蛋白質超過30%結構含有α螺旋結構。Lifson-Roig理論是一個用來描述胜肽的螺旋結構多寡的理論,其假設每個胺基酸形成螺旋的傾向不受胺基酸所在的位置影響。為了驗證這個假設,我們合成了一系列的胜肽,利用圓二色光譜儀測量此系列胜肽的螺旋程度,並且將胺基酸在6, 11和16號位置的w值求出。在6號和11號位置的w值很相近,但16號位置的w值卻非常的高。
為了探討胺基酸側鏈長短對w值的影響,我們利用固相胜肽合成技術設計並合成一系列含有精氨酸長度不同的非自然界胺基酸S-2-amino-6-guanidinohexanoic acid (Agh),S-2-amino-4-guanidino-butyric acid (Agb), S-2-amino-3-guanidinopropionic acid (Agp)和離氨酸長度不同的非自然界胺基酸Ornithine (Orn), S-2,4-diaminobutyric acid (Dab), S-2,3-diaminopropionic acid (Dap)並根據修飾過的 Lifson-Roig理論測量其w值。在精氨酸長度不同的非自然界胺基酸中,精氨酸的w值最高,顯示精氨酸形成螺旋的傾向最高。在離氨酸長度不同的非自然界胺基酸中,w值隨著側鏈長度增長而增加。 螺旋內離子對作用力可以穩定結構.側鏈長度與正負電荷相對間距會影響螺旋程度.為了研究側鏈長度對於影響程度的影響,利用固相胜肽合成技術合成並設計一系列含有合成出與精氨酸長度不同的非自然界胺基酸S-2-amino-6-guanidinohexanoic acid (Agh),S-2-amino-4-guanidino-butyric acid (Agb), S-2-amino-3-guanidinopropionic acid (Agp)以及與穀胺酸長度不同的天門冬胺酸的胜肽序列,包括AspAgh4, GluAgh4, AspAgb3, GluAgb3, AgpAsp5以及 AgpGlu5. 利用圓二色光譜儀測量不同胜肽在pH 2-12範圍下的螺旋程度。圓二色光譜儀測得訊號結果包括個別胺基酸本身對於螺旋喜好程度、胺基酸序列中側鏈之間與的作用力以及胺基酸側鏈與螺旋骨架N端C端作用力.本研究中,根據圓二色光譜儀訊號顯示pH 7情況下,螺旋程度大小依序為GluAgh4 > AspAgh4, GluAgb3 > AspAgb3, AgpGlu5 > AgpAsp5. 當負電荷胺基酸側鏈越長,其表現出的螺旋程度也相對較高。 | zh_TW |
dc.description.abstract | One third of all protein residues adopt a helical conformation. Statistical mechanical models such as modified Lifson-Roig theory are used to describe the conformational ensemble of monomeric helical peptides. One basic assumption in these statistical models is that the helix propensity for a given amino acid is position independent. To test this assumption, the helix propensity for neutral non-Ala residues at various guest positions were derived from circular dichroism spectroscopy (CD) data. Helix propensities were similar for positions 6 and 11 for the same amino acid, but much higher at position 16.
Helix propensity (w) for Arg and Lys analogs were derived based on modified Lifson-Roig theory to investigate the effect of Lys and Arg side chain length on helix formation. The helix propensity (w) for Arg analogs followed the trend: wArg > wAgh > wAgb > wAgp, indicating the uniqueness of the Arg side chain length in helix formation. In contrast, all three Lys analogs were energetically unfavorable for N-capping. Orn and Dap were energetically favorable for C-capping, whereas Dab was energetically unfavorable for C-capping. All three Lys analogs were energetically unfavorable at internal helix positions. Electrostatic ion pairing interactions between oppositely charged amino acids can stabilize proteins and helical structures. To study the effect of Glu side chain length and relative spacing on intrahelical ion pairing interaction, peptides AspAgh4, GluAgh4, AspAgb3, GluAgb3, AgpAsp5, and AgpGlu5 were synthesized and studied by CD at pH 2-12. Based on CD data at pH 7, the helical content of the peptides followed the trend GluAgh4 > AspAgh4, GluAgb3 > AspAgb3 and AgpGlu5 > AgpAsp5. The results showed that helicity increases with increasing side chain length of the negatively charged residue (Glu vs Asp). | en |
dc.description.provenance | Made available in DSpace on 2021-06-13T05:45:00Z (GMT). No. of bitstreams: 1 ntu-100-R98223154-1.pdf: 2523878 bytes, checksum: abd62dd7b358598b6b4618c189a9563e (MD5) Previous issue date: 2011 | en |
dc.description.tableofcontents | Table of Contents……………………………………………………I
List of Figures……………………………………………………………………………III List of Tables………………………………………………………………………………V List of Schemes…………………………………………………………………………VII Abbreviations……………………………………………………………………………VIII 誌謝………………………………………………………………………………..……X 中文摘要………………………………………………………………………………………XI Abstract……………………………………………………………………………………XIII Chapter 1.……..........................………………………………………………………1 I. Introduction………………………………………………………………………….1 I-1. Proteins…………………………………………………………….2 I-2.Electrostatics and Protein Structure Stability……………3 I-3. Hierarchical Nature of Protein Structures………………..5 I-4.The α-Helix………………………………………………..…….5 I-5. Short α-Helix Model Systems……………………………….9 I-6.Effect of Side Chain Length on Intrahelical Ion Pairing Interactions…………………………………………10 I-7. Thesis Overview………………………………………………..12 II. References…………………………………………………………………..……..13 Chapter 2.Positional Effects on Helical Ala-Based Peptides……………………22 I. Introduction…………………………………………………………………………23 II. Results and Discussion………………………………………………………….26 II-1.Deriving Helix Propensity (w), N-Capping Parameter (n), and C-Capping Parameter (c) for Ala, Gly, and Lys…………………………………………………26 II-2.Deriving Helix Propensity (w), N-Capping Parameter (n), and C-Capping Parameter (c) for Leu, Phe, and Pff at the Various Positions………………………………………..27 III. Conclusions……………………………………………………………………….30 IV. Acknowledgements……………………………………………………………..30 V. Experimental Section……………………………………………………………31 VI. References……………………………………………………………..………….31 Chapter 3.Helix Formation and Capping Energetics of Arginine and Lysine Analogues with Varying Side Chain Length………………………....39 I. Introduction………………………………………………………………………….40 II. Results and Discussion………………………………………………………….45 II-1Deriving Helix Propensity (w) for Arg Analogs…….....45 II-2.Peptide Design and Synthesis for Determining Helix Propensity (w), N-Capping Parameter (n), and C-Capping Parameter (c) for Lys Analogs……………...46 II-3.Circular Dichroism Spectroscopy of the Lys Analog-Containing Peptides……………………………..….49 II-4.Helix Formation Parameters for Lys Analogs……………51 III. Conclusions………………………………………………………………………52 IV. Acknowledgements……………………………………………………………..53 V. Experimental Section…………………………………………………………….54 VI. References…………………………………………………………………………64 Chapter 4.Effect of Side Chain Length on Intrahelical Ion Pairing Interactions……………………………………………………………………69 I. Introduction…………………………………………………………………………70 II. Results and Discussion………………………………………………………….72 II-1.Peptide Design and Synthesis for Investigating the Effect of Glu Side Chain Length on Intrahelical Ion Pairing Interactions…………………………………………….72 II-2.Circular Dichroism Spectroscopy (CD) ………………….82 III. Conclusions……………………………………………………………………….86 IV. Acknowledgements……………………………………………………………..87 V. Experimental Section……………………………………………………………87 VI. Appendix…………………………………………………………..……………..102 VII. References……………………………………………………………………….108 | |
dc.language.iso | en | |
dc.title | 麩胺酸側鏈長度於螺旋內離子對作用力的影響以及離胺酸側鏈長度和胺基酸位置對螺旋程度的影響 | zh_TW |
dc.title | Effect on Helical Content: Positional Effects, Lys and Arg Side Chain Length, and Glu Side Chain Length in Intrahelical Ion Pairs | en |
dc.type | Thesis | |
dc.date.schoolyear | 99-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 陳佩燁,黃人則 | |
dc.subject.keyword | α螺旋,胺基酸側鏈,離子對作用力,固相胜肽,合成, | zh_TW |
dc.subject.keyword | α-helix,helix propensity,solid phase peptide synthesis,amino acid side chain,ion-pairing interaction, | en |
dc.relation.page | 112 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2011-07-27 | |
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 |
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