عنوان

Molecular dynamics analyses of prion protein structures :

9789811088155

9811088152

9789811088148

9811088144

Molecular dynamics analyses of prion protein structures :

[Book]

the resistance to prion diseases down under /

Jiapu Zhang.

Singapore :

Springer,

2018.

1 online resource

Focus on structural biology ;

volume 10

Includes bibliographical references and index.

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)

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Unlike bacteria and viruses, which are based on DNA and RNA, prions are unique as disease-causing agents since they are misfolded proteins. Prion diseases are called "protein structural conformational? diseases. This monograph is the book on molecular dynamics (MD) simulations nearly for all the known normal prion protein (PrPC) PDB entries in the Protein Data Bank (PDB) and associations. Pig is a species that is largely resistant to prions, and chicken, turtles, frogs are species resisting prion infection too; firstly, this book will address all PrP strong immunity species (such as rabbits, dogs, horses, water buffaloes, pigs, chicken, turtles, frogs), compared with high susceptibility species. Other PrP models and doppel models are also MD studied in this book. Secondly, all the mutants of mouse PrP and human PrP are well studied by this book. Mouse mutations in the?2-?2 loop and the C-terminal will bring clear structures with highly and clearly ordered loop structures. Human mutations will cause prion diseases such as Creutzfeldt-Jakob diseases (CJDs), Gerstmann-Sträussler-Scheinker (GSS) syndrome, fatal familial insomnia (FFI), etc. Deep MD analyses of mouse and human mutants are done in this book. Thirdly, PrP binding with antibodies/compounds etc. is well MD studied in this book. The informatics of potential antiprion drugs known will be revealed. Lastly, cross-? structure PrP peptides are well studied. This book is ideal for practical computing staff in the fields of computational physics, computational biology, computational chemistry, biomedicine, bioinformatics, cheminformatics, materials, applied mathematics and theoretical physics, information technology, operations research, biostatistics, etc. As an accessible introduction to these fields, this book is also ideal as a teaching material for students.

Springer Nature

com.springer.onix.9789811088155

Molecular dynamics analyses of prion protein structures.

9789811088148

Prion diseases.

Life Sciences.

Proteomics.

HEALTH & FITNESS-- Diseases-- General.

MEDICAL-- Clinical Medicine.

MEDICAL-- Diseases.

MEDICAL-- Evidence-Based Medicine.

MEDICAL-- Internal Medicine.

Prion diseases.

HEA-- 039000

MED-- 014000

MED-- 022000

MED-- 045000

MED-- 112000

PSB

PSBC

Zhang, Jiapu

20200823223026.0

pn

[Book]

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