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研究生:程麗梅
研究生(外文):Lei-Mei Cheng
論文名稱:β摺版胜月太構形穩定度之分子模擬研究
論文名稱(外文):Examination of conformational stability for beta peptides using molecular modeling method
指導教授:孫英傑孫英傑引用關係
指導教授(外文):YIng-chieh Sun
學位類別:碩士
校院名稱:國立臺灣師範大學
系所名稱:化學研究所
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:115
中文關鍵詞:β摺版分子模擬胜月太構形
外文關鍵詞:beta peptidesmolecular modeling methodconformational stability
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ubiquitin是一個具有72個胺基酸的小蛋白質,整個分子的二級結構具有五股β摺版和一股α螺旋鏈,在N端位置上17個胺基酸的胜月太 片段則為兩股反平行的β摺版,且其在水溶液中能夠形成單一的β髮夾狀結構。我們使用GB/SA方法做分子動力學的模擬,研究β突起( β bulge )存在與否和置換折彎(turn)上胺基酸次序對ubiquitin N端之蛋白質胜月太片段的二級結構穩定性影響。模擬結果支持實驗的論點,顯示由Gly10形成的β bulge對ubiquitin蛋白質二級結構的維持有明顯的效應。而ubiquitin原先turn的次序(type I turn,TLTGK)對β髮夾結構的穩定性較優於其它常見折彎處次序為NG、AG、GD、NPDGT的胜月太片段。
在第二部分我們根據文獻所提出的NG turn能夠幫助兩股形成穩定的二級結構,設計了一小段胜月太 鏈,兩股上多為非極性胺基酸,從直線的結構做常溫300 K折疊模擬,於50 ps時產生β摺版的二級結構,且維持了1.6 ns以上,其穩定性與一實驗上所提出的結果相符。而在置換成GD次序後,胜月太 鏈的結構明顯變得不穩定,顯示此置換會影響骨架的二面角,支鏈的位向以及氫鍵的生成,甚至整個結構的穩定性。
最後,在研究整個蛇毒蛋白分子CTX2和CTX3的構形轉換上,我們使用Locally Enhanced Sampling方法(簡稱LES)模擬。利用LES方法可以多次複製以及自行選定複製區域的優點,克服骨架上能障較高的部位,成功地從CTX3轉換為CTX2構形。而CTX2並未完全轉換為CTX3結構,其因素包括:不佳的起始構形,Pro 30和Pro 33對β34骨架二面角之影響等,以及β34構形轉換受到兩旁β12和β5牽制的立體障礙等,文中將討論這些因素。

Ubiquitin is a protein of abundant experimental data for stability and folding/unfolding studies. It consists of five beta + one helix strands. The N-terminal segment of Res1-17 is one of the few cases where a short peptide can populate the monomeric beta hairpin conformation in aqueous solution. In the present study, we carried out molecular dynamics (MD) simulation to examine conformational stability for this peptide and its mutants using GB/SA solvation model. Delection of glycine at turn segment of this ubiquitin peptide destabilizes the β-hairpin as observed in experiment. In addition, we replaced the turn segment of TLTGK with several turn-location-favored segments, including NPDGT, NG, AG, and, GD, in this peptide. The simulation results shows that the TLTGK is more stable than NPDGT segment for this beta hairpin peptide, consistent with experimental observation. Other turn mutations also showed less stability compared with the original TLTGK segment in this ubiquitin peptide.
In addition, we carried out a folding MD simulation of a peptide of NG turn and non-polar residues on the strands at 300 K. Starting from unfolded structure, the trajectory showed that the beta hairpin formed at 50 ps and maintains up to 1.6 ns. The fast folding is consistent with experimental observation. With a mutation of GD segment with NG segment, the beta hairpin structure significantly destablized. The backbone dihedral angles, orientation of side chains and formation of hydrogen bonds will be reported and analyzed.
Finally, we examined the conformational transition between two cardiotoxins, CTX2 and CTX3, which differ six residues in their sequence. The simulation results show that the mutation from CTX3 to CTX2 can get close to CTX2 structure but not reverse. With implement of a locally enhanced sampling (LES) method, the conformational transition is enhanced to some extend. The factors influencing the simulated results, including presence of prolines, steric effect etc., will be
analyzed and discussed.

總目錄
圖目錄……………………………………………………….….…..…(v)
表目錄………………………………………………………………..(viii)
中文摘要………………………………………………………………(x)
英文摘要……………………………………………………………...(xii)
目錄
第壹章、 緒論
一、 前言…………………………………………………….……..1
二、 ubiquitin與相關peptide文獻回顧…………………………...2
1-2.1、ubiquitin結構………………………………………………....2
1-2.2、β-bulge的種類……………………………………….……....3
1-2.3、過去文獻所探討的β-bulge組合…………………….……..4
1-2.4、Gly10存在對ubiquitin整個蛋白質和胜月太片段在水溶液中構形的差異……………………………………………………………...5
1-2.5、ubiquitin結構對於mutation和pH值的影響……………….6
1-2.6、turn對hairpin folding的影響……………………………….7
1-2.7、β-hairpin在水中折疊的穩定度分析…………………………7
三、 LES方法之相關應用………………………………………...9
四、 研究動機…………………………………………………….10
1-4.1、ubiquitin:研究β-bulge的角色……………………………10
1-4.2、peptide 的設計:turn次序與兩股穩定性比較…………….10
1-4.3、LES方法用於CTX2和CTX3構形轉換…………………11
第貳章、 方法
模擬方法
2-1.1、分子動力學(MD)模擬與PME(Particle Meshed Ewald sum)
原理……………………………………………………..…12
2-1.2、GB/SA的原理..…………………………………………....15
2-1.3、LES(Locally Enhanced Sampling)的原理………….….17
分析方法
2-2.1、根均方偏差(RMSD)的原理……………………….….19
2-2.2、氫鍵的定義………………………………………….…….19
第參章、 方法
第一部份、ubiquitin與自行設計的peptide
3-1、ubiquitin N端的PME常溫模擬……………………….…..20
3-2、在不同力場下以GB/SA方法對U(1-17)W和deGU(1-16)W
的二級結構模擬比較…………………………………….….28
3-3、U(1-17)再折疊的動力學模擬…………………………...33
3-4、turn上位置以Gln和Leu置換Lys11………………..…….39
(1) U17K11Q軌跡結果討論…..…………………………….39
(2) U17K11L軌跡結果討論…..…………………………….41
3-5、比較同種類的turn 但不同氨基酸次序與兩股產生作用力
之穩定關係…………………………………………………..51
3-6、U(1-17)兩股上疏水效應的探討─Ala scan……………66
3-7、置換不同turn種類對U(1-17)整個分子結構的影響.….73
(1)U17NG的結果分析……………………………………....74
(2)U17AG的結果分析………………………………….…...75
(3)U17NG和U17AG兩者的比較……………………….….76
(4)U17GD的結果分析…………………………………..…..77
3-8、另一β髮夾胜月太 鏈之模擬………………………………………88
3-9、兩蛋白質CTX2和CTX3構形轉換之模擬………………..94
(1)NMR中CTX2和CTX3的差異…………………………94
(2)分區擾動的影響…………………………………….……95
(3)複製區域大小應用於CTX3轉變成CTX2………….….96
(4)CTX2轉換成CTX3的結果………………………….….96
第肆章、 總結………………………………………………………...106
第伍章、 參考文獻…………………………………………………..108
圖目錄
圖1.1 ubiquitin之二級結構圖…………………………………...….2
圖2.1 CTX2β34局部複製五次結構圖………………………..……17
圖2.2 降低LES能障的成因……………………………………….18
圖3-1.1 ubiquitin之NMR二級結構圖…………………………...….23
圖3-1.2 U(1-17)W和deGU(1-16)W的RMSD圖…………………..23
圖3-1.3 U(1-17)W之二面角圖………………………………..…….24
圖3-1.4 deGU(1-16)W之二面角圖………………………….…….…25
圖3-1.5 U(1-17)W和deGU(1-16)W二級結構比較圖……………...26
圖3-2.1 U(1-17)_gbsa_parm 94結構圖……………………………...30
圖3-2.2 deGU(1-16)_gbsa_parm 94結構圖……………………….…30
圖3-2.3 U(1-17)_parm 96的二級結構圖…………………………….32
圖3-2.4 U(1-17)和deGU(1-16)之parm 94的RMSD圖…….………31
圖3-2.5 U(1-17)和deGU(1-16)之parm 96的RMSD圖…….……….31
圖3-3.1 U(1-17)再折疊之RMSD圖…………………………...…….35
圖3-3.2 U(1-17)在不同溫度下在折疊情形…………………………36
圖3-3.3 U(1-17)在500K下的二面角圖………………………..….…37
圖3-4.1 U17上置換LYS11之RMSD值……………………..………43
圖3-4.2 U17K11L之二面角Res6~Res11圖…………………....……44
圖3-4.3 U17K11Q之二面角Res6~Res11圖…………………...……45
圖3-4.4 U17K11L軌跡個別氫鍵條狀圖………………….…………46
圖3-4.5 U17K11Q軌跡個別氫鍵條狀圖………………….………..47
圖3-5.1 S1∼S4軌跡之N17和N16折彎處RMSD值比較………..53
圖3-5.2 N17S1和N16S1軌跡氫鍵直條圖………………………….54
圖3-5.3 N17S2和N16S2軌跡氫鍵直條圖………………………….55
圖3-5.4 N17S3和N16S3軌跡氫鍵直條圖………………………….56
圖3-5.5 N17S4和N16S4軌7跡氫鍵直條圖………………………57
圖3-5.6 N17S1之二面角圖…………………………………………..58
圖3-5.7 N17S2之二面角圖…………………………………………..59
圖3-5.8 N17S3之二面角圖………………………………………….60
圖3-5.9 N17S4之二面角圖…………………………………………..61
圖3-6.1 以Ala取代兩股上重要氫鍵位置之RMSD值…………....68
圖3-7.1 U17NG、U17AG、U17GD之RMSD值…………………..79
圖3-7.2 U17NG之二面角圖…………………………………………80
圖3-7.3 U17AG之二面角圖…………………………………………81
圖3-7.4 U17GD之二面角圖…………………………………………82
圖3-7.5 U17NG與U17GD軌跡個別氫鍵直條圖………………….83
圖3-8.1 以NG當turn的三股和兩股的peptide………………….…90
圖3-8.2 DNA binding motif dimmer和其類似物…………………....90
圖3-8.3 bulge角色對圖3-8.2(B)之次序的影響………………….91
圖3-8.4 bulge角色對圖3-8.1(B)之次序的影響………….……...92
圖3-8.5 各條軌跡的RMSD值比較………….……………….……..93
圖3-9.1 由CTX3轉換成CTX2之單區與分區擾動比較………...102
圖3-9.2 複製區域對CTX3轉變成CTX2的影響………………...103
圖3-9.3 CTX2轉變成CTX3再不同複製區域的結果……………104
圖3-9.4 C3muC2_R9之loop2的rmsd圖…………………………105
表目錄
表3-1.1 U(1-17)W和deGU(1-16)W的軌跡氫鍵比較………….…..27
表3-2.1 U(1-17)_parm96之軌跡氫鍵百分比….………………….…32
表3-2.2 deGU(1-16)_parm96之軌跡氫鍵百分比……………...……32
表3-3.1 U17在不同溫度下再折疊之軌跡氫鍵………………….….38
表3-4.1 U17K11L單一裂片300K模擬二級結構比較表………...…48
表3-4.2 U17K11Q單一裂片300K模擬二級結構比較表………..…49
表3-4.3 U17K11L和U17K11Q軌跡氫鍵……………………….….50
表3-5.1 N17S1和N16S1之氫鍵百分比……………………….….....62
表3-5.2 N17S2和N16S2之氫鍵百分比……………………………..63
表3-5.3 N17S3和N16S3之氫鍵百分比…………………………....64
表3-5.4 N17S4和N16S4之氫鍵百分比……………………….…...65
表3-6.1 U17mut4A下模擬的二級結構…………………………..…69
表3-6.2 U17R5R13mutA下模擬的二級結構…………………...…..70
表3-6.3 U17R3R15mutA下模擬的二級結構…………………….....71
表3-6.4 U17R3R15mutA軌跡的氫鍵…………………………….....72
表3-7.1 U17NG單一片段之二級結構……………………………....84
表3-7.2 U17AG單一片段之二級結構……………………………....85
表3-7.3 U17GD單一片段之二級結構……………………………....86
表3-7.4 U17NG和U17GD軌跡氫鍵比較……………………..…..87
表3-9.1 檢視CTX2和CTX3構形轉換之模擬軌跡……………....98
表3-9.2 台灣眼鏡蛇心臟毒蛋白CTX1∼CTX5的氨基酸次序…..99
表3-9.3 CTX2和CTX3之β34片段的NMR二級結構比較…..…100
表3-9.4 CTX2和CTX3之β34之NMR片段結構氫鍵比較…….101
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