Molecular Structures And Structural Dynamics Of Prion Proteins And Prions
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Molecular Structures And Structural Dynamics Of Prion Proteins And Prions
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Author : Jiapu Zhang
language : en
Publisher: Springer
Release Date : 2015-09-14
Molecular Structures And Structural Dynamics Of Prion Proteins And Prions written by Jiapu Zhang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-09-14 with Science categories.
This monograph is the first easy-to-read-and-understand book on prion proteins' molecular dynamics (MD) simulations and on prions' molecular modelling (MM) constructions. It enables researchers to see what is crucial to the conformational change from normal cellular prion protein (PrPC) to diseased infectious prions (PrPSc), using MD and MM techniques. As we all know, prion diseases, caused by the body's own proteins, are invariably fatal and highly infectious neurodegenerative diseases effecting humans and almost all animals for a major public health concern. Prion contains no nucleic acids and it is a misshapen or conformation-changed protein that acts like an infectious agent; thus prion diseases are called “protein structural conformational” diseases. PrPC is predominant in α-helices but PrPSc are rich in β-sheets in the form as amyloid fibrils; so very amenable to be studied by MD techniques. Through MD, studies on the protein structures and the structural conversion are very important for revealing secrets of prion diseases and for structure-based drug design or discovery. Rabbits, dogs, horses and buffaloes are reported to be the few low susceptibility species to prion diseases; this book's MD studies on these species are clearly helpful to understand the mechanism underlying the resistance to prion diseases. PrP(1-120) usually has no clear molecular structures; this book also studies this unstructured region through MD and especially MM techniques from the global optimization point of view. This book is ideal for practitioners in computing of biophysics, biochemistry, biomedicine, bioinformatics, cheminformatics, materials science and engineering, 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.
Molecular Dynamics Analyses Of Prion Protein Structures
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Author : Jiapu Zhang
language : en
Publisher: Springer
Release Date : 2018-07-20
Molecular Dynamics Analyses Of Prion Protein Structures written by Jiapu Zhang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-07-20 with Science categories.
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.
Optimization Based Molecular Dynamics Studies Of Sars Cov 2 Molecular Structures
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Author : Jiapu Zhang
language : en
Publisher: Springer Nature
Release Date : 2023-10-16
Optimization Based Molecular Dynamics Studies Of Sars Cov 2 Molecular Structures written by Jiapu Zhang and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-10-16 with Science categories.
COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized. This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data. To gain a thorough understanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored. This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.
Recent Advances In Crystallography
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Author : Jason B. Benedict
language : en
Publisher: BoD – Books on Demand
Release Date : 2012-09-19
Recent Advances In Crystallography written by Jason B. Benedict and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-09-19 with Science categories.
The advent of X-ray diffraction in the early twentieth century transformed crystallography from an area of scientific inquiry largely limited to physics, mineralogy, and mathematics, to a highly interdisciplinary field which now includes nearly all life and physical sciences as well as materials science and engineering. This book is a collection of works showcasing some of the most recent developments in the field of crystallography.
Molecular Biology Of Assemblies And Machines
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Author : Alasdair Steven
language : en
Publisher: Garland Science
Release Date : 2016-02-18
Molecular Biology Of Assemblies And Machines written by Alasdair Steven and has been published by Garland Science this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-02-18 with Medical categories.
Molecular Biology of Assemblies and Machines provides a comprehensive narrative of the ways in which macromolecular structures assemble and how they interact with other complexes and organelles in the cell. Richly illustrated in full color, the text is written for advanced undergraduates, graduate students, and researchers in biochemistry, molecular biology, biophysics, cell biology, chemistry, structural biology, immunology, microbiology, and medicine.
Advanced Understanding Of Neurodegenerative Diseases
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Author : Raymond Chuen-Chung Chang
language : en
Publisher: BoD – Books on Demand
Release Date : 2011-12-16
Advanced Understanding Of Neurodegenerative Diseases written by Raymond Chuen-Chung Chang and has been published by BoD – Books on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-12-16 with Medical categories.
Advanced Understanding of Neurodegenerative Diseases focuses on different types of diseases, including Alzheimer's disease, frontotemporal dementia, different tauopathies, Parkinson's disease, prion disease, motor neuron diseases such as multiple sclerosis and spinal muscular atrophy. This book provides a clear explanation of different neurodegenerative diseases with new concepts of understand the etiology, pathological mechanisms, drug screening methodology and new therapeutic interventions. Other chapters discuss how hormones and health food supplements affect disease progression of neurodegenerative diseases. From a more technical point of view, some chapters deal with the aggregation of prion proteins in prion diseases. An additional chapter to discuss application of stem cells. This book is suitable for different readers: college students can use it as a textbook; researchers in academic institutions and pharmaceutical companies can take it as updated research information; health care professionals can take it as a reference book, even patients' families, relatives and friends can take it as a good basis to understand neurodegenerative diseases.
Biochemistry
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Author : Donald Voet
language : en
Publisher: John Wiley & Sons
Release Date : 2010-11-16
Biochemistry written by Donald Voet and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-11-16 with Science categories.
The "Gold Standard" in Biochemistry text books, Biochemistry 4e, is a modern classic that has been thoroughly revised. Don and Judy Voet explain biochemical concepts while offering a unified presentation of life and its variation through evolution. Incorporates both classical and current research to illustrate the historical source of much of our biochemical knowledge.
Non Fibrillar Amyloidogenic Protein Assemblies Common Cytotoxins Underlying Degenerative Diseases
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Author : Farid Rahimi
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-01-13
Non Fibrillar Amyloidogenic Protein Assemblies Common Cytotoxins Underlying Degenerative Diseases written by Farid Rahimi and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-01-13 with Medical categories.
Amyloid-forming proteins are implicated in over 30 human diseases. The proteins involved in each disease have unrelated sequences and dissimilar native structures, but they all undergo conformational alterations to form fibrillar polymers. The fibrillar assemblies accumulate progressively into disease-specific lesions in vivo. Substantial evidence suggests these lesions are the end state of aberrant protein folding whereas the actual disease-causing culprits likely are soluble, non-fibrillar assemblies preceding the aggregates. The non-fibrillar protein assemblies range from small, low-order oligomers to spherical, annular, and protofibrillar species. Oligomeric species are believed to mediate various pathogenic mechanisms that lead to cellular dysfunction, cytotoxicity, and cell loss, eventuating in disease-specific degeneration and systemic morbidity. The particular pathologies thus are determined by the afflicted cell types, organs, systems, and the proteins involved. Evidence suggests that the oligomeric species may share structural features and possibly common mechanisms of action. In many cases, the structure–function interrelationships amongst the various protein assemblies described in vitro are still elusive. Deciphering these intricate structure–function correlations will help understanding a complex array of pathogenic mechanisms, some of which may be common across different diseases albeit affecting different cell types and systems.
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes
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Author : Adam Liwo
language : en
Publisher: Springer
Release Date : 2018-12-19
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes written by Adam Liwo and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-19 with Technology & Engineering categories.
This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.
Prion Proteins
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Author : Jörg Tatzelt
language : en
Publisher: Springer
Release Date : 2011-09-15
Prion Proteins written by Jörg Tatzelt and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-09-15 with Science categories.
Genetics of Prion Disease, by S. Lloyd, S. Mead and J. Collinge. Atypical Prion Diseases in Humans and Animals, by M. A. Tranulis, S. L. Benestad, T. Baron and H. Kretzschmar. Chronic Wasting Disease, by S. Gilch, N. Chitoor, Y. Taguchi, M. Stuart, J. E. Jewell and H. M. Schätzl. Transgenic Mouse Models and Prion Strains, by G. C. Telling. Neuroprotective and Neurotoxic Signaling by the Prion Protein, by U. K. Resenberger, K. F. Winklhofer and J. Tatzelt. Prion Seeded Conversion and Amplification Assays, by C. D. Orrú and B. Caughey. Prion Protein and Its Conformational Conversion: A Structural Perspective, by W. K. Surewicz and M. I. Apostol. Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations, by M.W. van der Kamp and V. Daggett. Chemical Biology of Prion Protein: Tools to Bridge the In Vitro/Vivo Interface, by R. Seidel and M. Engelhard. The PrP-Like Proteins Shadoo and Doppel, by D. Westaway, N. Daude, S. Wohlgemuth and P. Harrison. Fungal Prions: Structure, Function and Propagation, by M. F. Tuite, R. Marchante and V. Kushnirov.