Molecular Dynamics Analyses of Prion Protein Structures

Description

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 β2-α2 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-β 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. Front Matter ....Pages i-xxix Basic Knowledge (Jiapu Zhang)....Pages 1-12 Front Matter ....Pages 13-15 Rabbits: Wild-Type and Mutants (Jiapu Zhang)....Pages 17-66 Dogs: Wild-Type and D159N Mutant (Jiapu Zhang)....Pages 67-79 Horses, Buffaloes, and Pigs (Jiapu Zhang)....Pages 81-98 Chicken, Turtles, and Frogs (Jiapu Zhang)....Pages 99-116 Other Species (Jiapu Zhang)....Pages 117-152 Front Matter ....Pages 153-154 Wild-Type Mouse 37 ∘C and 19.85 ∘C Structures (Jiapu Zhang)....Pages 155-165 Mouse Mutants (Jiapu Zhang)....Pages 167-190 Other Species with an Ordered β2-α2 Loop (Jiapu Zhang)....Pages 191-203 Front Matter ....Pages 205-206 Human Mutants (Jiapu Zhang)....Pages 207-243 Human PrPC Monomer, Dimer and Its M129V Mutant (Jiapu Zhang)....Pages 245-262 Human Peptides (Jiapu Zhang)....Pages 263-270 Front Matter ....Pages 271-271 PrP Bounded to Antibodies, Nanobody, RNA Aptamer, etc. (Jiapu Zhang)....Pages 273-295 Potential Antiprion Drugs (Jiapu Zhang)....Pages 297-303 Front Matter ....Pages 305-306 Mathematical Formulas for All PrP Peptides’ Cross-β Structures (Jiapu Zhang)....Pages 307-345 Hydrogen Bonds Between Two Optimized Fundamental Chains of Each Model (Jiapu Zhang)....Pages 347-353 Back Matter ....Pages 355-375