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研究生:洪仕偉
研究生(外文):Hung, Shih-Wei
論文名稱:分子動力學模擬蛇毒蛋白於混合自組裝單分子膜吸附現象
論文名稱(外文):Studies of Cardiotoxin Proteins Adsorption onto Mixed Self-Assembled Monolayers using Molecular Dynamics Simulation
指導教授:錢景常蕭百沂
指導教授(外文):Chieng, Ching-ChangHsiao, Pai-Yi
學位類別:博士
校院名稱:國立清華大學
系所名稱:工程與系統科學系
學門:工程學門
學類:核子工程學類
論文種類:學術論文
論文出版年:2012
畢業學年度:100
論文頁數:54
中文關鍵詞:分子動力學模擬自組裝單分子膜蛇毒蛋白蛋白質吸附自由能計算
外文關鍵詞:molecular dynamics simulationself-assembled monolayercardiotoxinprotein adsorptionfree energy calculation
相關次數:
  • 被引用被引用:0
  • 點閱點閱:183
  • 評分評分:
  • 下載下載:22
  • 收藏至我的研究室書目清單書目收藏:0
蛋白質於固體表面的吸附現象在生醫工程應用上,例如醫療植入、生醫檢測晶片、藥物釋放系統以及組織工程,扮演相當重要的角色。在此研究中,我們利用了分子動力學模擬來研究蛇毒蛋白於混合不同長度的硫醇自組裝單分子膜上的吸附現象。藉由計算蛋白質與自組裝單分子膜的吸附能,我們可以得知其吸附強度。由模擬結果我們也探討了影響蛋白質吸附的物理機制。
除了靜態特性,我們也研究了蛋白質脫附的動態資訊,例如脫附力、蛋白質結構變化、作用能量以及平均力勢能。我們利用拉伸分子動力學模擬來研究蛋白質於自組裝單分子膜的脫附過程。在此研究中我們也將利用Jarzynski恆等式於非平衡態模擬下估計的平均力勢能與傳統的平衡態模擬的傘型取樣方法作比較,並探討模擬中所使用的拉伸速度以及取樣數目對利用Jarzynski恆等式估計平均力勢能的精準度的影響。
最後,我們研究蛇毒蛋白於混合不同長度的硫醇混合自組裝單分子膜上的吸附自由能。我們發現吸附自由能可藉由混合不同長度的硫醇所形成的混合自組裝單分子膜提升。利用成分分析,我們可以分別出在不同混合比例表面上,驅動其吸附的主因是由自組裝單分子膜表面或是水溶液分子而來。另外我們也進行了熱力學分項分析,如自由能、焓以及熵,此分析可幫助我們更為了解驅動蛋白質吸附的主要物理機制。
Understanding the protein adsorption onto solid surface is of critical importance in the field of bioengineering, such as medical implants, diagnostic biosensors, drug delivery systems, and tissue engineering. This study proposed molecular dynamics (MD) simulations to investigate the physical mechanism of cobra cardiotoxin (CTX) proteins adsorption on alkanethiol self-assembled monolayers (SAMs) composed of S(CH2)5CH3 and S(CH2)9CH3. The binding energy of the CTX protein to the SAM surface of different mixing ratios of alkanethiol chains was calculated. The physical mechanisms are examined to understand how these parameters affect the adsorption of a CTX protein on SAM surfaces.
Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single CTX protein from SAM surface was investigated by means of steered molecular dynamics (SMD) simulations. By applying Jarzynski’s equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski’s equality, were compared with the conventional umbrella sampling method.
The free energies of a CTX protein adsorption onto SAMs with different mixing ratios were investigated. Enhancement of the adsorption affinity, i.e., the change in free energy of adsorption, for mixed SAMs was determined. A component analysis conducted to quantify the physical mechanisms that promoted CTX adsorption revealed contributions from both SAMs and the solvent. Further component analyses of thermodynamic properties, such as the free energy, enthalpy, and entropy, indicated that the contribution from SAMs was driven by enthalpy, and the contribution from the solvent was driven by entropy.
摘 要 i
Abstract ii
致 謝 iii
Contents iv
List of Figures vi
1. Introduction 1
2. Model System and Methodology 5
2.1. Simulation Model 5
2.2. Potential Energy Function 6
2.3. Initial Configuration 7
2.4. Simulation Procedure 8
2.5. PMF Calculation 9
2.5.1. PMF Calculation Using the Umbrella Sampling Method 10
2.5.2. PMF Calculation Using Jarzynski’s Equality 11
3. Results and Discussions 15
3.1. Static Properties of CTX Adsorption 15
3.1.1. Comparison of Results Using Different Solvent Models 15
3.1.2. Binding Energy of a CTX Protein on SAM Surface 17
3.1.3. Physical Mechanisms of CTX Adsorption 18
3.2. Dynamic Information of CTX Desorption Process 25
3.2.1. Structural Changes of CTX during the Desorption Process 25
3.2.2. Adsorption Force during the Desorption Process 26
3.2.3. Energetics of the Desorption Process 29
3.2.4. PMF Calculated by the Umbrella Sampling Method 31
3.2.5. PMF Estimations Based upon Jarzynski’s Equality 32
3.3. Adsorption Free Energies of CTX onto Various SAMs 36
3.3.1. Structural Changes of CTX Adsorption 36
3.3.2. Adsorption Free Energies of CTX Adsorption 36
3.3.3. Energetics of CTX Adsorption 39
3.3.4. Thermodynamics of CTX Adsorption 41
4. Conclusion 45
5. References 47
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