Molecular Structures And Structural Dynamics Of Prion Proteins And Prions

Author : Jiapu Zhang
Publisher : Springer
Page : 355 pages
File Size : 55,8 Mb
Release : 2015-09-14
Category : Science
ISBN : 9789401773188

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Molecular Structures and Structural Dynamics of Prion Proteins and Prions by Jiapu Zhang Pdf

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.

Author : Jiapu Zhang
Publisher : Springer
Page : 375 pages
File Size : 40,6 Mb
Release : 2018-07-20
Category : Science
ISBN : 9789811088155

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Molecular Dynamics Analyses of Prion Protein Structures by Jiapu Zhang Pdf

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.

Author : Jörg Tatzelt
Publisher : Springer
Page : 304 pages
File Size : 50,6 Mb
Release : 2011-09-15
Category : Science
ISBN : 9783642240676

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Prion Proteins by Jörg Tatzelt Pdf

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.

Author : Jiapu Zhang
Publisher : Springer Nature
Page : 956 pages
File Size : 46,8 Mb
Release : 2023-10-16
Category : Science
ISBN : 9783031367731

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Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures by Jiapu Zhang Pdf

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.

Author : Jorg Tatzelt
Publisher : Unknown
Page : 80 pages
File Size : 48,8 Mb
Release : 2010
Category : Prions
ISBN : 0954333527

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The Prion Protein by Jorg Tatzelt Pdf

A conformational transition of the cellular prion protein (PrPC) into an aberrantly folded isoform designated scrapie prion protein (PrPSc) is the hallmark of a variety of neurodegenerative disorders collectively called prion diseases. They include Creutzfeldt-Jakob disease and Gerstmann-Stäussler-Scheinker syndrome in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle and chronic wasting disease (CWD) in free-ranging deer. In contrast to the deadly properties of misfolded PrP, PrPC seems to possess a neuroprotective activity. More-over, animal models indicated that the stress-protective activity of PrPC and the neurotoxic effects of PrPSc are somehow interconnected. In this timely book, leading scientists in the field have come together to highlight the apparently incongruous activities of different PrP conformers. The articles outline current research on celluar pathways implicated in the formation and signaling of neurotoxic and physiological PrP isoforms and delineate future research direction. Topics covered include the physiologcial activity of PrPC and its possible role as a neurotrophic factor, the finding that aberrant PrP conformers can cause neurodegeneration in the absence of infectious prion propagation, the requirement of the GPI anchor of PrPC for the neurotoxic effects of scrapie prions, the pathways implicated in the formation and neurotoxic properties of cytosolically localized PrP, the impact of metal ions on the processing of PrP, and the role of autophagy in the propagation and clearance of PrPSc. The book is fully illustrated and chapters include comprehensive reference sections. Essential reading for scientists involved in prion research.

Author : Joaquín Castilla,Jesús R. Requena
Publisher : MDPI
Page : 211 pages
File Size : 51,9 Mb
Release : 2018-11-07
Category : Electronic books
ISBN : 9783038973089

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PrPSc Prions: State of the Art by Joaquín Castilla,Jesús R. Requena Pdf

This book is a printed edition of the Special Issue "PrP^Sc prions: state of the art" that was published in Pathogens

Author : Maria Lurdes Pinto,Maria Anjos Pires,Leonor Orge,Jesus R. Requena
Publisher : Frontiers Media SA
Page : 157 pages
File Size : 45,6 Mb
Release : 2021-02-26
Category : Science
ISBN : 9782889665198

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The Design of Molecular Tools in Relation to Prions and their Biosafety by Maria Lurdes Pinto,Maria Anjos Pires,Leonor Orge,Jesus R. Requena Pdf

Author : Adam Liwo
Publisher : Springer
Page : 851 pages
File Size : 54,7 Mb
Release : 2018-12-19
Category : Technology & Engineering
ISBN : 9783319958439

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo Pdf

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.

Author : Moselio Schaechter
Publisher : Academic Press
Page : 1200 pages
File Size : 41,6 Mb
Release : 2010-04-19
Category : Science
ISBN : 9780080961286

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Desk Encyclopedia of Microbiology by Moselio Schaechter Pdf

The Desk Encyclopedia of Microbiology, Second Edition is a single-volume comprehensive guide to microbiology for the advanced reader. Derived from the six volume e-only Encyclopedia of Microbiology, Third Edition, it bridges the gap between introductory texts and specialized reviews. Covering topics ranging from the basic science of microbiology to the current "hot" topics in the field, it will be invaluable for obtaining background information on a broad range of microbiological topics, preparing lectures and preparing grant applications and reports. * The most comprehensive single-volume source providing an overview of microbiology to non-specialists * Bridges the gap between introductory texts and specialized reviews. * Provides concise and general overviews of important topics within the field making it a helpful resource when preparing for lectures, writing reports, or drafting grant applications

Author : Beat Hörnlimann,Detlev Riesner,Hans A. Kretzschmar
Publisher : Walter de Gruyter
Page : 743 pages
File Size : 48,7 Mb
Release : 2007
Category : Medical
ISBN : 9783110182750

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Prions in Humans and Animals by Beat Hörnlimann,Detlev Riesner,Hans A. Kretzschmar Pdf

This comprehensive work, aimed at both students and researchers alike, systematically covers all aspects of prion diseases (transmissible spongiform encephalopathies), from their history, microbiology and pathology to their transmissibility and prevention. The book describes diseases such as Creutzfeldt-Jakob disease, kuru, mad cow disease (BSE), chronic wasting disease and scrapie, highlighting their biochemical, molecular biological, genetic, and clinical aspects. A detailed presentation of the impact of prion diseases in fields such as pharmaceutics, blood products, disinfection, surgical instruments and epidemiology concludes with a discussion of preventive measures. A renowned editorial team, representing the fields of medicine, veterinary medicine and molecular biology, brought together 80 internationally respected authors for this translation and new edition of the successful German publication, not only from relevant research fields, but also from industry and public health institutions. The book includes chapters by, among many other notable scientists, William J. Hadlow, who discovered the relationship between the human and animal forms of prion diseases and Michael P. Alpers, with 45 years of experience in Papua New Guinea investigating the first known human epidemic form, kuru, transmitted by endocannibalism.Further contributions fromGerald A. H. Wells, a veterinary pathologist who described BSE and recognised its similarity to scrapie, thus recording the first cases in 1986 of the most important animal epidemic of modern times, and Robert G. Will, a medical neurologist and epidemiologist who discovered the emergence of the variant form of Creutzfeldt-Jakob disease in 1996, underscore the strength of this author team. Carefully edited with numerous illustrations, this work offers a systematic approach committed to a clear presentation of the current knowledge of prion diseases. It aims to inspire and stimulate interdisciplinary cooperation, innovative research ideas and effective prevention.

Author : Donald Voet,Judith G. Voet
Publisher : John Wiley & Sons
Page : 1526 pages
File Size : 46,5 Mb
Release : 2010-12-01
Category : Science
ISBN : 9780470570951

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Biochemistry by Donald Voet,Judith G. Voet Pdf

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.

Author : Vladimir N. Uversky,Anthony Fink
Publisher : Springer Science & Business Media
Page : 538 pages
File Size : 43,9 Mb
Release : 2007-05-26
Category : Medical
ISBN : 9780387365343

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Protein Misfolding, Aggregation and Conformational Diseases by Vladimir N. Uversky,Anthony Fink Pdf

The second volume continues to fill the gap in protein review and protocol literature. It does this while summarizing recent achievements in the understanding of the relationships between protein misfoldings, aggregation, and development of protein deposition disorders. The focus of Part B is the molecular basis of differential disorders.

Author : Sylvain Lehmann,Jacques Grassi
Publisher : Springer Science & Business Media
Page : 240 pages
File Size : 45,6 Mb
Release : 2004-11-22
Category : Medical
ISBN : 3764324155

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Techniques In Prion Research by Sylvain Lehmann,Jacques Grassi Pdf

-There is an acceleration in prion disease research because of the spread of mad cow disease. -This book covers in vitro, cellular, and animal models adapted for the study of TSEs. -Includes bio-saftey procedures.

Author : Cláudio M. Gomes,Jinghui Luo,Wolfgang Hoyer
Publisher : Frontiers Media SA
Page : 193 pages
File Size : 52,5 Mb
Release : 2023-07-19
Category : Science
ISBN : 9782832529799

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The biochemistry of amyloids in neurodegenerative diseases, volume II by Cláudio M. Gomes,Jinghui Luo,Wolfgang Hoyer Pdf

Author : Ivo Nikolaev Sirakov
Publisher : BoD – Books on Demand
Page : 84 pages
File Size : 49,9 Mb
Release : 2019-01-30
Category : Medical
ISBN : 9781789850178

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Prions by Ivo Nikolaev Sirakov Pdf

The cellular prion protein (PrPC) is expressed as a cell surface protein mainly in the central and peripheral nervous system. The discovery that prions are infectious agents changed the concept of protein synthesis in modern biology and built a bridge between the genesis of infectious and genetic diseases. This book discusses the normal function of the PrPC and its modulatory role in synaptic mechanisms. It describes the pathophysiological processes that accompany TSE - neurotoxicity, loss of anti-inflammatory protective function, neuronal death including prion-induced autophagy and apoptosis, and accumulation of PrPSc in the cytoplasm of neurons. Another aspect outlined here is that some prion diseases show strain variations that determine their development, demonstrating their key role in the development and progression of TSE.