Intro; Preface; Acknowledgments; Contents; About the Author; Acronyms; 1 Basic Knowledge; 1.1 Molecular Dynamics (MD); 1.2 MD Simulation Methods; 1.2.1 Initialization; 1.2.2 Heating the System; 1.2.3 Equilibration; 1.2.4 Production Phase; 1.3 MD Analysis Methods; 1.4 Quantum Mechanics/Molecular Mechanics (QM/MM); 1.5 Optimization Methods Used in MD, QM; 1.6 Protein, Prion Protein and Prion; Part I Prion Resistance Species; Introduction; 2 Rabbits: Wild-Type and Mutants; 2.1 The Wild-Type NMR Structure (PDB Entry 2FJ3); 2.1.1 MD at 300K; 2.1.2 MD at 350K; 2.1.3 MD at 450K

2.2 The Wild-Type X-ray Structure (PDB Entry 3O79)2.2.1 MD at 300K; 2.2.2 MD at 350K; 2.2.3 MD at 450K; 2.2.4 A Concluding Remark; 2.3 The I214V Mutant (NMR Structure PDB Entry 2JOM); 2.3.1 MD at 300K; 2.3.2 MD at 350K; 2.3.3 MD at 450K; 2.4 The S173N Mutant (NMR Structure PDB Entry 2JOH, X-ray Structure PDB Entry 4HMM); 2.4.1 MD at 300K; 2.4.2 MD at 350K; 2.4.3 MD at 450K; 2.5 The S170N Mutant (X-ray Structure PDB Entry 4HLS); 2.5.1 MD at 300K; 2.5.2 MD at 350K; 2.5.3 MD at 450K; 2.6 The S170N and S174N Mutants (X-ray Structure PDB Entry 4HMR); 2.6.1 MD at 300K; 2.6.2 MD at 350K

2.6.3 MD at 450K2.7 The Structure Without the Disulfide Bond (SS) (Homology Structure); 3 Dogs: Wild-Type and D159N Mutant; 3.1 The Wild-Type NMR Structure (PDB Entry 1XYK); 3.1.1 MD at 300K; 3.1.2 MD at 350K; 3.1.3 MD at 450K; 3.2 The D159N Mutant (Homology Structure); 3.2.1 MD at 300K; 3.2.2 MD at 350K; 3.2.3 MD at 450K; 4 Horses, Buffaloes, and Pigs; 4.1 Horse's Wild-Type NMR Structure (PDB Entry 2KU4); 4.1.1 MD at 300K; 4.1.2 MD at 350K; 4.1.3 MD at 450K; 4.2 Buffalo's Homology Structure; 4.2.1 MD at 300K; 4.2.2 MD at 350K; 4.2.3 MD at 450K

4.3 Pig's Wild-Type NMR Structure (PDB Entry 1XYQ)4.3.1 MD at 300K; 4.3.2 MD at 350K; 4.3.3 MD at 450K; 5 Chicken, Turtles, and Frogs; 5.1 Chicken's Wild-Type NMR Structure (PDB Entry 1U3M); 5.1.1 MD at 300K; 5.1.2 MD at 350K; 5.1.3 MD at 450K; 5.2 Turtle's Wild-Type NMR Structure (PDB Entry 1U5L); 5.2.1 MD at 300K; 5.2.2 MD at 350K; 5.2.3 MD at 450K; 5.3 Frog's Wild-Type NMR Structure (PDB Entry 1XU0); 5.3.1 MD at 300K; 5.3.2 MD at 350K; 5.3.3 MD at 450K; 6 Other Species; 6.1 Syrian Hamster's Wild-Type NMR Structure (PDB Entry 1B10); 6.2 Bovine

6.2.1 The Wild-Type NMR Structure (PDB Entry 1DWY)6.2.2 The N-Terminal PrP(1-30) (PDB Entry 1SKH); 6.3 Sheep, Ovine, Ovis Aries; 6.3.1 The Wild-Type X-ray Structure (PDB Entry 1UW3); 6.3.2 The Sheep Q168H Mutant (PDB Entry 1XYU) at 300K in Low or Neutral pH Environments); 6.3.3 The Sheep PrPC(135-155) (PDB Entry 1S4T); 6.3.4 The Sheep PrPC(142-166) with Mutation Y155A/R156A (PDB Entries 2RMV/W); 6.3.4.1 Sheep PrPC(142-166) Y155A Mutant (PDB Entry 2RMV); 6.3.4.2 Sheep PrPC(142-166) R156A Mutant (PDB Entry 2RMW)