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研究生： 魏忠誠
論文名稱： 具多帶電殘基胜鏈折疊之分子動力學模擬
指導教授： 孫英傑
學位類別： 碩士
Master
系所名稱： 化學系
Department of Chemistry
論文出版年： 2005
畢業學年度： 93
語文別： 中文
論文頁數： 82
中文關鍵詞： 分子動力學模擬
論文種類： 學術論文
相關次數： 點閱：194  下載：0 
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    • 摘要
    　　芋螺毒素Conantokin-T（Con-T）是一條由21個胺基酸所組成的短螺旋胜鏈，含有5個螺旋轉折，並含有10個帶電胺基酸，而本研究利用分子動力學模擬，已檢視此胜鏈之折疊路徑與預測其折疊時間。於300 K下，18條軌跡中，有16條折疊至折疊態，且顯示平均折疊時間約為50 ns。其他2條軌跡在200 ns內未折疊至折疊態。軌跡分析結果顯示，在折疊一開始的幾奈秒，Tyr5，Met8，與Leu9的疏水叢聚（hydrophobic cluster）可協助殘基5–9先行形成螺旋，又因N、C端的帶電殘基所造成的電荷–電荷作用力，使得胜鏈產生U型的中間態。經過10 ns，打破數個非活性電荷–電荷作用力之後，主要出現在此一步驟的非活性作用力為Gla10–Lys18（這代表Gla10與Lys18間的鹽橋）與／或Gla10–Lys19，使得胜鏈產生J型的中間態。在16條折疊成功軌跡中，有7條經過約15 ns可折疊至折疊態；而其他9條經過約30 ns會到達另一個L型中間態，其含有4個螺旋轉折與1個Arg13、Gla14處的扭結。此L型中間態約需要額外的15 ns以折疊至折疊態。此外，上述的前7條軌跡其折疊時間皆小於45 ns，而後9條之折疊時間則皆大於45 ns，造成約50 ns的平均折疊時間。在2條未折疊成功的軌跡中，其主要中間態分別是由5與6個帶電殘基所形成的電荷叢聚（charge cluster）所穩定。我們所預測的折疊時間約50 ns，比相同長度之alanine-based胜鏈的折疊時間82 ns為短，顯示這種含有許多帶電殘基的折疊能障比alanine-based胜鏈稍小。

    Abstract
    A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 run 300 K trajectories, 16 trajectories folded, with an averaged folding time of ~50 ns. 2 trajectories did not fold in up to 200 ns simulation. An analysis of the trajectories showed that, at the beginning of a few ns, helix formation started from residues 5-9 with assistance of a hydrophobic clustering involving Tyr5, Met8, and Leu9. The peptide formed a U-shape mainly due to charge-charge interactions between charged residues at the N- and C- terminus segments. In the next ~10 ns, several non-native charge-charge interactions were broken and non-native Gla10-Lys18 (this denotes a salt bridge between Gla10 and Lys18) and/or Gla10-Lys19 interactions appeared more frequently in this folding step and the peptide became a fishhook J-shape. From this structure, the peptide folded to the folded state in 7 of all 16 folded trajectories in ~15 ns. Alternatively, in ~30 ns, they can make the con-T in a L-shape with 4 helical turns and a kink at the Arg13 and Gla14 segment in 9 folded trajectories. Con-T in the L-shape then required another ~15 ns to fold into the folded state. In addition, in overall folding times, the former 7 trajectories folded faster with the total folding times all shorter than 45 ns while the latter 9 trajectories folded at a time longer than 45 ns, resulting in an average folding time of ~50 ns. Two major folding intermediates found in 2 non-folded trajectories are stabilized by charge clusters of 5 and 6 charged residues, respectively. The predicted folding time of ~50 ns, which is shorter than the folding time of 82 ns for an alanine-based peptide of the same length, suggests that the energy barrier of folding for this type of peptide with many charged residues is smaller than alanine-based helical peptides slightly.

    目錄 第一章、緒論……………………………………………………………1 1–1、前言…………………………………………………………………2 1–2、芋螺毒素Conantokin-T（Con-T）之結構………………………3 1–3、影響α螺旋穩定度的因素…………………………………………6 1–4、蛋白質的折疊模型與折疊熱力學…………………………………7 1–5、利用分子動力學模擬輔助了解蛋白質折疊問題………………11 1–6、本論文的研究目標………………………………………………12 第二章、方法……………………………………………………………13 2–1、分子動力學模擬簡介……………………………………………14 2–2、GB/SA內涵水合模型簡介………………………………………19 2–3、非天然胺基酸分子力場之建立…………………………………20 2–4、模擬程序…………………………………………………………23 2–5、RMSD值及構形簇分析…………………………………………27 2–6、骨幹氫鍵分析……………………………………………………29 2–7、疏水叢聚分析……………………………………………………31 2–8、鹽橋分析…………………………………………………………33 第三章、結果與討論……………………………………………………34 3–1、Con-T之恆溫模擬結果及折疊態結構…………………………35 3–2、Con-T再折疊模擬之RMSD值與構形簇分析…………………36 3–3、Con-T再折疊之路徑……………………………………………41 3–4、骨幹氫鍵的形成…………………………………………………43 3–5、疏水效應…………………………………………………………55 3–6、鹽橋………………………………………………………………64 3–7、未折疊軌跡中發現的中間態結構………………………………72 3–8、Con-T之360 K的模擬…………………………………………74 第四章、結論……………………………………………………………76 第五章、參考文獻………………………………………………………78

    第五章、參考文獻

    1. see, for example, Eaton, W. A.; Munoz, V.; Hagen S. J.; Jas, G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J. Annu. Rev. Biophys. Biomol. Strut. 2000, 29, 327.
    2. Chen, R. P.; Huang, J. J.; Chen, H. L.; Jan H.; Velusamy M.; Lee, C. T.; Fann, W.; Larsen, R. W.; Chan S. I. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7305.
    3. Chen, P. Y.; Gopalacushina, B. G.; Yang, C. C.; Chan, S. I.; Evans, P. A. Protein Science 2001, 10, 2063.
    4. Gnanakaran, S.; Nymeyer, H.; Portman; J.; Sanbonmatsu, K. Y.; Garcia, A. E. Curr. Opin. Struct. Biol. 2003, 13, 168.
    5. Chowdhury, S; Lee, M. C.; Xiong, G.; Duan, Y. J. Mol. Biol. 2003, 327, 711.
    6. Chowdhury, S; Lee, M.C.; Xiong, G.; Duan, Y. J. Phys. Chem. B 2003, 108, 13855.
    7. Chowdhury, S.; Zhang, W.; Wu, C.; Xiong, G.; Duan, Y. Biopolymers 2003, 68, 63.
    8. Simmerling, C.; Strockbine, B.; Roitberg, A. E. J. Am. Chem. Soc. 2002, 124, 11258.
    9. Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13898.
    10. Vila, J. A.; Ripoll, D. R.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 14812.
    11. Zhou, R. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13280.
    12. Chowdhury, S.; Lee, M. C.; Duan, Y. J. Phys. Chem. B 2004, 108, 13855.
    13. Liwo, A.; Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362.
    14. Duan, Y. Kollman, P. A. Science 1998, 282, 740.
    15. Pande, V. S.; Baker, I.; Chapman, J.; Elmer, S. P.; Khaliq, S.; Larson, S. M.; Rhee, Y. M.; Shirts, M. R.; Snow, C. D.; Sorin, E. J.; Zagrovic, B. Biopolymers 2003, 68; 91.
    16. Ferrara, P.; Apostolakis, J.; Caflisch, A. Proteins 2002, 39, 252.
    17. Nymeyer, H.; Garcia, A. E. Proc. Natl. Acad. Sci. U.S.A. 2003, 100; 13934.
    18. Pak, Y.; Jang, S.; Shin, S. J. Am. Chem. Soc. 2002, 124, 4976.
    19. Pak, Y.; Kim, E.; Jang, S. J. Chem. Phys. 2004, 121, 9184.
    20. Snow, C. D. ; Zagrovic, B.; Pande, V. S. J. Am. Chem. Soc. 2002, 124, 14548.
    21. Sung, S. S. Biophys. J. 1999, 76, 164.
    22. Wang, H. Sung, S. S. J. Am. Chem. Soc. 2000, 122, 1999.
    23. Snow, C. D.; Sorin, E. J.;Rhee, Y. M.; Pande, V. S. Ann. Rev. Biophys. Biomol. Stru. 2005, 34, 43.
    24. Islam, S. A.; Karplus, M.;Weaver, D. L. Structure 2004, 12, 1833.
    25. Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. J. Phys. Chem. B 2005, 109, 8220.
    26. Elber, R. Curr. Opin. Struct. Biol. 2005, 15, 151.
    27. Herges, T.; Wenzel, W. Structure 2005, 13, 661.
    28. Sorin, E. J.; Pande, V. S. J. Comput. Chem. 2005, 26, 682.
    29. Liwo, A.; Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362.
    30. Ulmschneider, J. P.; Jorgensen, W. L. J. Am. Chem. Soc. 2004, 126, 1849.
    31. Shea, J. E.; Onuchic, J. N.; Brooks, C. L., III. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16064.
    32. Li, F. Y.; Chen, Y.; You, Z. Q.; Mou, C. Y. J. Chin. Chem. Soc. 2002, 49, 783.
    33. Lei, H.; Duan, Y.; J. Chem. Phys. 2004, 121, 12104.
    34. Garcia, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782.
    35. DeMarco, M. L.; Alonso, D. O. V.; Daggett, V. J. Mol. Biol. 2004, 341, 1109.
    36. Chowdhury, S.; Lei, H.; Duan, Y. J. Phys. Chem. B 2005, (in press).
    37. Cavalli, A.; Ferrara, P.; Caflisch, A. Proteins 2002, 47, 305.
    38. Hummer, G.; Garcia, A. E.; Garde, S. Proteins 2001, 42, 77.
    39. (a) Williams, S.; Causgrove, T. P., Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691. (b) Thompson, P.; Eaton, W.; Hofrichter, J. Biochemistry 1997, 36, 9200.
    40. Skjrbk, N.; Nielsen, K. J.; Lewis, R. J.; Alewood, P.; Craik, D. J. J. Biol. Chem. 1997, 272, 2291.
    41. Lin, C. H.; Chen, C. S.; Hsu, K. S.; King, D. S.; Lyu, P. C. FEBS Lett. 1997, 407, 243.
    42. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham III, T. E.; Wang, J.; Ross, W. S.; Simmerling, C.; Darden, T. Merz, K. M.;. Stanton, R. V.; Cheng, A.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G.. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. Amber7 Users’ Manual 2002. (San Francisco: University of California; San Francisco).
    43. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Ang R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. J. Comput. Chem. 2003, 24, 1999.
    44. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V.G.; Montgomery, Jr., J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople. J. A. Gaussian 98 User’s Reference 1998.
    45. Tsui, V.; Case, D. A. Biopolymers 2001, 56, 275.
    46. Daura, X.; van Gunsteren, W. F.; Mark, A. E. Proteins 1999, 34, 269.
    47. Aurora, R.; Creamer, T. P.; Srinivasan, R.; Rose, G. D. J. Biol. Chem. 1997, 272, 1413.
    48. Radford, S. E. Trends Biochem. Sci. 2000, 25, 611.
    49. Nelson, D. L. and Cox, M. M. In Lehninger Principles of Biochemistry 3rd ed. pp.159-199, 2000, Published by Worth Publishers.
    50. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
    51. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Comput. Phys. 1984, 81, 3684.
    52. Dyson, H. J. et al. J. Mol. Biol. 1988, 201, 161.

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