| 摘要 | 第1-7页 |
| Abstract | 第7-13页 |
| Chapter 1 Introduction | 第13-17页 |
| ·Quantum chemistry and biomolecular simulation | 第13-15页 |
| ·Issues in protein interactions | 第15-17页 |
| Chapter 2 Theory and method | 第17-29页 |
| ·Overview | 第17页 |
| ·Quantum Mechanics | 第17-22页 |
| ·Hartree-Fock (HF) | 第18-19页 |
| ·Density Functional Theory (DFT) | 第19-20页 |
| ·Polarizable Continuum Model (PCM) | 第20-22页 |
| ·Generalized Born (GB) Solvation Model | 第22页 |
| ·Molecular Mechanics and AMBER Force Field | 第22-23页 |
| ·Polarized Protein-Specific Charges (PPC) | 第23-26页 |
| ·Polarized nucleic acid-Specific Charges (PNC) | 第26-29页 |
| Chapter 3 Activation mechanism study of glucokinase by M197V mutation | 第29-41页 |
| ·Introduction | 第29-32页 |
| ·Theory and methods | 第32-34页 |
| ·Protein construction and MD simulation | 第32-33页 |
| ·DCCM | 第33页 |
| ·Calculation of binding free-energy | 第33-34页 |
| ·Results and discussion | 第34-39页 |
| ·The effect on conformation by M197V mutation | 第34-38页 |
| ·The effect on binding affinity by M197V mutation | 第38-39页 |
| ·Conclusion | 第39-41页 |
| Chapter 4 Molecular dynamics simulation of non-specific and specific LacI-DNA complex | 第41-57页 |
| ·Introduction | 第41-42页 |
| ·Computational Methods | 第42-43页 |
| ·MD simulation | 第42-43页 |
| ·Calculation of binding free-energy | 第43页 |
| ·Result and discussion | 第43-54页 |
| ·The conformation analysis of non-specific and specific complex | 第43-45页 |
| ·The total hydrogen bond analysis for non-specific and specific complex | 第45-47页 |
| ·The affinity difference between the non-specific and specific complex | 第47-54页 |
| ·The affinity between Prod_1 and Prod_2 | 第54页 |
| ·Conclusion | 第54-57页 |
| Chapter 5 Molecular dynamics study of DNA binding by INT-DBD under polarized force field | 第57-73页 |
| ·Introduction | 第57-59页 |
| ·Computational Methods | 第59-61页 |
| ·MD simulation | 第59-60页 |
| ·Binding free energy calculation | 第60-61页 |
| ·Result and discussion | 第61-70页 |
| ·Conformational analysis | 第61-64页 |
| ·Binding free energy of INT-DBD and DNA | 第64-67页 |
| ·Dynamics of Protein-DNA hydrogen bonds | 第67-70页 |
| ·Conclusion | 第70-73页 |
| Chapter 6 Interaction Specific Binding Hotspots in Endonuclease Colicin-Immunity ProteinComplex from IMD Simulations | 第73-89页 |
| ·Introduction | 第73-75页 |
| ·Theoretical Methods | 第75-77页 |
| ·MD simulation | 第75-76页 |
| ·Calculation of binding free-energy | 第76-77页 |
| ·Results and discussion | 第77-87页 |
| ·Dynamic stability of the E9-Im9 complex | 第77-78页 |
| ·Inter-protein hydrogen bonds in E9-Im9 complex | 第78-82页 |
| ·Effect of D51A mutation on stability of E9-Im9 complex | 第82-84页 |
| ·Effect of Y54A mutation on stability of E9-Im9 complex | 第84页 |
| ·Effect of Y55A mutation on stability of E9-Im9 complex | 第84-85页 |
| ·Binding energies calculated under standard AMBER force field | 第85-87页 |
| ·Conclusion | 第87-89页 |
| Reference | 第89-101页 |
| RELATED PUBLICATIONS | 第101-102页 |
| Acknowledgement | 第102-103页 |
