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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：174  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

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