台灣眼鏡蛇毒液心臟毒蛋白是一個具有60個胺基酸殘基，結構上僅具由五個β股所形成的雙股與三股β摺板二級結構，分子中有四個雙硫鍵連接分子的骨架結構。本論文利用升溫分子動力學模擬方法以檢視鹼性的台灣眼鏡蛇毒CTXⅢ於水溶液中展開的情形。模擬的結果顯示，於天然結構中所形成β1與β2間的氫鍵，於計算平衡結構時就不再形成，因此說明於CTXⅢ中β1-β2形成的雙股β摺板較β3-β4-β5所形成的三股β摺板結構不穩定，此模擬得到現象與實驗得到的結果相符合；可能因為三股β摺板間的氫鍵間的合作效應較雙股β摺板結構間的氫鍵明顯，而幫助穩定三股β摺板的結構。另外根據RMSD、二維構形簇、氫鍵的分析並觀察模擬軌跡中之結構變化得到的資訊，建議CTXⅢ的展開在β1與β2的結構展開後，可能經由兩個主要的路徑展開；此二可能路徑為經過β3與β4間的氫鍵先斷或是β3與β5間的氫鍵先斷的的中間態，由於可能的氫鍵之合作效應作用於兩兩β股間的氫鍵，因此得到此二中間態。另外計算所有軌跡之非極性胺基酸支鏈的旋度半徑之後並建議於摺疊的先期發現有疏水聚集的效應。並透過計算α螺旋的二級結構，建議於展開路徑中可能形成α螺旋結構之CTXⅢ的胺基酸片段。本論文中另外亦對計算與實驗的結果相關性進行討論。最後，我們亦進行了CTXⅡ與R36A CTXⅢ變異的模擬，這些結果並與得到的CTXⅢ結果進行比較，希望這些資料可以幫助對CTXⅢ展開的了解。

Thermal denaturation molecular dynamics simulation of cardiotoxin III from Taiwan cobra venom in solution were carried out to examine the unfolding of this small basic protein of 60 amino acids. The simulations showed that the hydrogen bonds between b1-b2 sheet loosed in the computed equilibrium structure, showing that the stability of b1-b2 sheet is weaker than b3-b5 sheet, consistent with experimental results. This should be due to the larger cooperation effect of hydrogen bonds in the latter larger b-sheet. Based on the results of RMSD, 2D-conformational analysis, breaking/formation of H-bonds, and observation of structure along the computed MD trajectories, the present simulations suggest that the unfolding of CTX III might go through two main pathways: after the b1-b2 sheet turns into a loop, either the hydrogen bonds between b3 and b4 strands or the b3 and b5 strands break first due to the cooperative effect of hydrogen bonds between two strands. Calculation of radius of gyration for non-polar residues along the trajectories suggests a hydrophobic clustering in the early stage of folding. A calculation of a-helix structure in the unfolding trajectories gave the segments of residues which may form a-helix in the folding/unfolding pathway(s). Other calculated results were correlated with experimental results and discussed. Finally, we carried out the simulations for CTX II and R36A CTX III mutant as well. The results were discussed and compared with the results of CTX III, and hope these results give a better understanding of the unfolding of CTXs.

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