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.
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.
Using Computer Modeling To Study Prion Diseases
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Author : Shan Dai
language : en
Publisher:
Release Date : 2011
Using Computer Modeling To Study Prion Diseases written by Shan Dai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Amyloid diseases, such as Parkinson's, Huntington's and Transmissible spongiform encephalopathy(Prion), have captured considerable public attention recently; all involve the aggregation of proteins in "misfolded" forms. The prion phenomenon, as one kind of amy- loid diseases, has gained scientific interest for its non-nuclei acid based, self-replication process: the disease-causing prion protein(PrPS̳c̳, also called the scrapie prion protein) can engender reproduction by inducing the normal prion protein(PrPC̳) to misfold its structure into the scrapie form; the PrPS̳c̳ itself acts as a template for the PrPC̳ during the reproduction process, and specific nucleic acid sequences are not involved during the reproduction. These properties were also discovered in several non-Mendelian heritable elements in the yeast Saccharomyces cerevisiae[1], thus the term "prion" was spread to certain yeasts and fungi. Rather, the characteristic disease strain information is hypothesized to be stored in the misfolded protein conformation. Elucidating the process of conversion from PrPC̳ to PrPS̳c̳ is essential in understanding and finding methods to cure the prion diseases. However, this is very challenging due to the lack of high-resolution experimental data of the PrPS̳c̳ structure, because of its insoluble and noncrystalline character. Accordingly, computer simulation of theoretical models for the protein structures presents a path forward for understanding and guiding experiment. We examine here with all atom molecular dynamics the unfolding of a proposed left-handed beta helix model for conversion of PrPC̳ to PrPS̳c̳[2]. In this thesis the prion protein aggregation is studied primarily in two regions: The first one is finding a common transition state between the alpha helical structure(AH) at the C-terminus of human PrPC̳ and the metastable left-handed beta helical(LHBH) structure which can possibly template human PrPS̳c̳ by performing the unfolding simulations to both structures. With molecular dynamics at high temperature 498K, two-dimensional projection of C[a̳l̳p̳h̳a̳] RMSD plots, cluster analysis, conformational analysis and alignments, the convergence to a common conformation intermediate between the AH and LHBH was observed, which indicates a direct pathway between the two structures without the need to pass through a fully unfolded structure. This result gives us new insights to the conversion between PrPC̳ and PrPS̳c̳. The second one is to search for prion regions in proteins of the Saccharomyces cerevisiae yeasts, using software developed by a collaborator which can propose potential matches of sequence to LHBH structure[3]. This method is based upon a heuristic variant of the dynamic programming (HDP) algorithm used in protein sequence alignment. We scanned 19 proteins proposed to have possible prion behavior in yeast, and used GPU based, explicit solvent, all atom molecular dynamics to assess their stability. Of the 19 starting proteins 9 were identified as being strong candidates for LHBH structure. Our computational studies using theoretical model on the prion protein aggregation, not only present a microscopic picture of the structural change of the prion proteins, but also may provide insights to the formation of the prion diseases and relevant drug design. These methods are also applicable in choosing good candidates of aggregation prone sequences in proteins before conducting real experiments, thus possibly saving budgets and time in the lab.
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 Interactions Computational Methods Analysis And Applications
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Author : M Michael Gromiha
language : en
Publisher: World Scientific
Release Date : 2020-03-05
Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-03-05 with Science categories.
This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Testing Recently Developed Molecular Dynamics Protocols For Structure Prediction Of Polypeptides And Prion Proteins
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Author : Timothy Click
language : en
Publisher:
Release Date : 2007
Testing Recently Developed Molecular Dynamics Protocols For Structure Prediction Of Polypeptides And Prion Proteins written by Timothy Click and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Molecular dynamics categories.
Dynamics Of Proteins And Nucleic Acids
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Author :
language : en
Publisher: Elsevier
Release Date : 2013-08-14
Dynamics Of Proteins And Nucleic Acids 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 2013-08-14 with Science categories.
Published continuously since 1944, Advances in Protein Chemistry and Structural Biology has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. Covers reviews of methodology and research in all aspects of protein chemistry Brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics
Proteins
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Author : Charles L. Brooks
language : en
Publisher: John Wiley & Sons
Release Date : 2009-09-08
Proteins written by Charles L. Brooks 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 2009-09-08 with Science categories.
Presenting a wide-ranging view of current developments in protein research, the papers in this collection, each written by highly regarded experts in the field, examine various aspects of protein structure, functions, dynamics, and experimentation. Topics include dynamical simulation methods, the biological role of atom fluctuations, protein folding, influences on protein dynamics, and a variety of analytical techniques, such as X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. This is part of a series devoted to providing general information on a wide variety of topics in chemical physics in order to stimulate new research and to serve as a text for beginners in a particular area of chemical physics.
Protein Structure And Dynamics Studied By Molecular Dynamics Simulations
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Author : Tim Meyer
language : en
Publisher:
Release Date : 2008
Protein Structure And Dynamics Studied By Molecular Dynamics Simulations written by Tim Meyer and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with categories.
Proteins In Solution And At Interfaces
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Author : Juan M. Ruso
language : en
Publisher: John Wiley & Sons
Release Date : 2013-01-31
Proteins In Solution And At Interfaces written by Juan M. Ruso 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 2013-01-31 with Science categories.
Explores new applications emerging from our latest understanding of proteins in solution and at interfaces Proteins in solution and at interfaces increasingly serve as the starting point for exciting new applications, from biomimetic materials to nanoparticle patterning. This book surveys the state of the science in the field, offering investigators a current understanding of the characteristics of proteins in solution and at interfaces as well as the techniques used to study these characteristics. Moreover, the authors explore many of the new and emerging applications that have resulted from the most recent studies. Topics include protein and protein aggregate structure; computational and experimental techniques to study protein structure, aggregation, and adsorption; proteins in non-standard conditions; and applications in biotechnology. Proteins in Solution and at Interfaces is divided into two parts: Part One introduces concepts as well as theoretical and experimental techniques that are used to study protein systems, including X-ray crystallography, nuclear magnetic resonance, small angle scattering, and spectroscopic methods Part Two examines current and emerging applications, including nanomaterials, natural fibrous proteins, and biomolecular thermodynamics The book's twenty-three chapters have been contributed by leading experts in the field. These contributions are based on a thorough review of the latest peer-reviewed findings as well as the authors' own research experience. Chapters begin with a discussion of core concepts and then gradually build in complexity, concluding with a forecast of future developments. Readers will not only gain a current understanding of proteins in solution and at interfaces, but also will discover how theoretical and technical developments in the field can be translated into new applications in material design, genetic engineering, personalized medicine, drug delivery, biosensors, and biotechnology.