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Table Of Contents

2.1. Protein Tyrosine Phosphatase 1B
2.1.1. Biological Significance of PTP1B
2.1.2. Tertiary Structure and Catalytic Mechanism of PTP1B
2.1.3. PTP Signature Motif (P-Loop)
2.1.4. WPD loop
2.2. Effect of Water Molecules on the PTP1B Conformation
3. METHODS
3.1. Molecular Dynamics Simulations
3.1.1. CHARMM Force Field
3.1.2. NAMD
3.1.3. MD Simulation Structures and Parameters
3.2. Trajectory Analysis
3.2.1. Root Mean Square Deviations (RMSD)
3.2.2. Mean Square Fluctuations (MSF)
3.2.3. Hydrogen Bond Criteria
3.2.4. Probability Distribution
4. RESULTS AND DISCUSSION
4.1. PTP1B in the unliganded WPDopen state
4.1.1. Structural Analysis of the WPDopen Simulations
4.1.2. Analysis of the Residue Fluctuations in the WPDopenSimulations
4.1.3. Polar Interactions between WPD loop and R-Loop
4.2. PTP1B in the unliganded WPD loop closed (WPDclosed) state
4.2.1. Structural Analysis of the WPDclosed Simulations
4.2.2. Analysis of the Dynamics of the WPDclosed Simulations
4.3. PTP1B in the Liganded WPDclosed State
5. CONCLUSIONS AND RECOMMENDATIONS
5.1. Conclusions
APPENDIX B: VMD COMMANDS FOR THE SELECTION OF ACTIVE SITE WATERS
APPENDIX C: ADDITIONAL ANALYSES FOR LIGANDED WPDCLOSED SIMULATIONS
APPENDIX D: SCRIPTS USED IN THE THESIS
D.1. Distance Measurement
D.2. Angle Measurement between Three Atoms
D.3. Dihedral Angle Measurement
D.4. RMSD Measurement
D.5. MSF Measurement
D.6. Energy Measurement
D.7. Hydrogen Bond Measurement
D.8. Solvent Accessible Surface Area Measurement
D.9. Water Counting
D.10. Probability Distribution
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Published by: ouchmet on Jan 17, 2012
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