Molecular Dynamics Analyses Of Prion Protein Structures
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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.
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.
Methods In Protein Structure And Stability Analysis Vibrational Spectroscopy
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Author : Vladimir N. Uversky
language : en
Publisher: Nova Publishers
Release Date : 2007
Methods In Protein Structure And Stability Analysis Vibrational Spectroscopy written by Vladimir N. Uversky and has been published by Nova Publishers this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Science categories.
Protein research is a frontier field in science. Proteins are widely distributed in plants and animals and are the principal constituents of the protoplasm of all cells, and consist essentially of combinations of a-amino acids in peptide linkages. Twenty different amino acids are commonly found in proteins, and serve as enzymes, structural elements, hormones, immunoglobulins, etc., and are involved throughout the body, and in photosynthesis. This book gathers new leading-edge research from throughout the world in this exciting and exploding field of research.
Concepts And Experimental Protocols Of Modelling And Informatics In Drug Design
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Author : Om Silakari
language : en
Publisher: Academic Press
Release Date : 2020-11-05
Concepts And Experimental Protocols Of Modelling And Informatics In Drug Design written by Om Silakari and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-11-05 with Medical categories.
Concepts and Experimental Protocols of Modelling and Informatics in Drug Design discusses each experimental protocol utilized in the field of bioinformatics, focusing especially on computer modeling for drug development. It helps the user in understanding the field of computer-aided molecular modeling (CAMM) by presenting solved exercises and examples. The book discusses topics such as fundamentals of molecular modeling, QSAR model generation, protein databases and how to use them to select and analyze protein structure, and pharmacophore modeling for drug targets. Additionally, it discusses data retrieval system, molecular surfaces, and freeware and online servers. The book is a valuable source for graduate students and researchers on bioinformatics, molecular modeling, biotechnology and several members of biomedical field who need to understand more about computer-aided molecular modeling. - Presents exercises with solutions to aid readers in validating their own protocol - Brings a thorough interpretation of results of each exercise to help readers compare them to their own study - Explains each parameter utilized in the algorithms to help readers understand and manipulate various features of molecules and target protein to design their study
Protein Misfolding And Proteostasis Impairment In Aging And Neurodegeneration From Spreading Studies To Therapeutic Approaches
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Author : Claudia Duran-Aniotz
language : en
Publisher: Frontiers Media SA
Release Date : 2022-10-05
Protein Misfolding And Proteostasis Impairment In Aging And Neurodegeneration From Spreading Studies To Therapeutic Approaches written by Claudia Duran-Aniotz and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-10-05 with Science categories.
Advances In Protein Chemistry And Structural Biology
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Author :
language : en
Publisher: Academic Press
Release Date : 2014-03-11
Advances In Protein Chemistry And Structural Biology written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-03-11 with Science categories.
This eclectic volume features two major topics: applications of mass spectrometry in bioscience; and computational methods for analysis of protein structure and interactions with other macromolecules. Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. - Describes advances in application of powerful techniques in a wide bioscience area - Chapters are written by authorities in their field - Targeted to a wide audience of researchers, specialists, and students - The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables
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.
Protein Folding Dynamics And Stability
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Author : Prakash Saudagar
language : en
Publisher: Springer Nature
Release Date : 2023-05-27
Protein Folding Dynamics And Stability written by Prakash Saudagar and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-27 with Science categories.
This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
Prion Proteins
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Author :
language : en
Publisher: Elsevier
Release Date : 2001-07-10
Prion Proteins written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2001-07-10 with Science categories.
Prion Proteins is "issue-oriented" and edited by a well-known authority in the field. Topics covered include structure, diversity, and energetics as well as the diseases associated with prion proteins.