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研究生: 陳紹弘
Chen, Shao-Hong
論文名稱: 生物鈉鈣離子通道交換機制之探討
A Study of the Sodium Calcium Ion Exchange Mechanism in NCX
指導教授: 劉晉良
Liu, Jinn-Liang
口試委員:
學位類別: 碩士
Master
系所名稱: 南大校區系所調整院務中心 - 應用數學系所
應用數學系所(English)
論文出版年: 2015
畢業學年度: 103
語文別: 中文
論文頁數: 30
中文關鍵詞: 鈉鈣離子交換通道分子動力模擬離子通道
外文關鍵詞: NCX_Mj, VMD, ion channels
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  • 生物細胞鈉鈣離子交換通道,是以極快的速度讓鈣離子由細胞內與鈉離子交換至細胞外。本研究利用Poisson-Fermi之理論分析NCX(sodium calcium exchanger)之離子結合構造,使我們能夠以數學的方式探討鈉鈣離子在NCX的交換機制,並成功的解釋鈉鈣離子交換之實驗結果。


    Biological sodium calcium ion exchange channel (NCX) removes calcium ions very rapidly from cell inside in exchange with sodium ions from outside. The Poisson-Fermi theory is used to analyze the binding potentials of NCX. It allows us to mathematically investigate the sodium-calcium ion exchange mechanism in NCX. Numerical results have been shown to agree with the experimental results of the sodium-calcium ion exchange.

    1.緒論1 2.下載PDB和PQR1 2.1.PDB1 2.2.PQR2 3.建構鈉離子與鈣離子通道2 3.1.建構出NCX的蛋白質2 3.2.結合點的位置3 3.3.找出各切層的通道中心5 3.4.使用VMD修正座標與半徑6 3.5. 鈉離子與鈣離子通道7 4.鈣鈉離子交換機制8 4.1.NCX的變形結構8 4.2.計算結合點電位能9 4.3.離子交換機制流程12 5.結論14 附錄15 程式碼1:繪製NCX平面圖(MATLAB)15 程式碼2:繪製通道立體圖(MATLAB)21 程式碼3:計算結合點電位能(C++)23 程式碼4:建構NCX(C++)26 參考文獻30

    1. J. Liao, H. Li, W. Zeng, D. B. Sauer, R. Belmares, Y. Jiang, Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger, Science 335, 686 (2012).
    2. D. W. Hilgemann, D. A. Nicoll, K. D. Philipson, Charge movement during Na+ translocation by native and cloned cardiac Na+/Ca2+ exchanger, Nature 352, 715 (1991).
    3. Protein Data Bank in Europe http://www.ebi.ac.uk/pdbe/
    4. T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J.H. Jensen, G. Klebe, N.A. Baker, PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations, Nucl. Acids Res. 35, W522–W525 (2007).
    5. PDB2PQR Server http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/
    6. H.-J. Hsieh, Potential profiles inside the X-shape channel of NCX_Mj, National Hsinchu University of Education (2014).
    7. D.S. He, A Graphic Study of Biological Sodium Calcium Ion Exchange Channel, National Hsinchu University of Education (2015).
    8. Visual Molecular Dynamics http://www.ks.uiuc.edu/Research/vmd/
    9. J.-L. Liu, B. Eisenberg, Poisson-Nernst-Planck-Fermi theory for modeling biological ion channels, The Journal of Chemical Physics 141, 22D532 (2014).

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