Molecular Dynamics Analyses Of Prion Protein Structures

Author : Jiapu Zhang
Publisher : Springer
Page : 375 pages
File Size : 48,8 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 : Jiapu Zhang
Publisher : Springer
Page : 355 pages
File Size : 55,6 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 : Serafin Fraga,J. M. Robert Parker,Jennifer M. Pocock
Publisher : Berlin : Springer-Verlag
Page : 304 pages
File Size : 42,5 Mb
Release : 1995
Category : Amino acid sequence
ISBN : UCSD:31822021096862

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Computer Simulations of Protein Structures and Interactions by Serafin Fraga,J. M. Robert Parker,Jennifer M. Pocock Pdf

Author : Jiapu Zhang
Publisher : Springer Nature
Page : 956 pages
File Size : 52,8 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 : Jörg Tatzelt
Publisher : Springer
Page : 304 pages
File Size : 46,5 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 : Kenneth M.Jr. Merz,Scott M. LeGrand
Publisher : Springer Science & Business Media
Page : 585 pages
File Size : 50,8 Mb
Release : 2012-12-06
Category : Science
ISBN : 9781468468311

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The Protein Folding Problem and Tertiary Structure Prediction by Kenneth M.Jr. Merz,Scott M. LeGrand Pdf

A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.

Author : M Michael Gromiha
Publisher : World Scientific
Page : 424 pages
File Size : 47,9 Mb
Release : 2020-03-05
Category : Science
ISBN : 9789811211881

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Protein Interactions: Computational Methods, Analysis And Applications by M Michael Gromiha Pdf

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.

Author : Om Silakari,Pankaj Kumar Singh
Publisher : Academic Press
Page : 398 pages
File Size : 43,9 Mb
Release : 2020-11-05
Category : Medical
ISBN : 9780128205471

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Concepts and Experimental Protocols of Modelling and Informatics in Drug Design by Om Silakari,Pankaj Kumar Singh Pdf

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

Author : Claudia Duran-Aniotz,Ines Moreno-Gonzalez,Rodrigo Morales,Danilo Bilches Medinas
Publisher : Frontiers Media SA
Page : 265 pages
File Size : 54,8 Mb
Release : 2022-10-05
Category : Science
ISBN : 9782889746071

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Protein Misfolding and Proteostasis Impairment in Aging and Neurodegeneration: From Spreading Studies to Therapeutic Approaches by Claudia Duran-Aniotz,Ines Moreno-Gonzalez,Rodrigo Morales,Danilo Bilches Medinas Pdf

Author : Anonim
Publisher : Elsevier
Page : 368 pages
File Size : 47,8 Mb
Release : 2013-08-14
Category : Science
ISBN : 9780124116276

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Dynamics of Proteins and Nucleic Acids by Anonim Pdf

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

Author : Anonim
Publisher : Academic Press
Page : 488 pages
File Size : 42,6 Mb
Release : 2014-03-11
Category : Science
ISBN : 9780128003732

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Advances in Protein Chemistry and Structural Biology by Anonim Pdf

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

Author : Gertz I. Likhtenshtein
Publisher : Springer Nature
Page : 523 pages
File Size : 54,9 Mb
Release : 2021-10-21
Category : Science
ISBN : 9783030825034

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Biological Water by Gertz I. Likhtenshtein Pdf

This book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.

Author : Vladimir N. Uversky
Publisher : Nova Publishers
Page : 326 pages
File Size : 50,7 Mb
Release : 2007
Category : Circular dichroism
ISBN : 1600217036

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Methods in Protein Structure and Stability Analysis: Vibrational spectroscopy by Vladimir N. Uversky Pdf

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.

Author : Anonim
Publisher : Elsevier
Page : 430 pages
File Size : 55,8 Mb
Release : 2006-10-06
Category : Science
ISBN : 0080522548

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Amyloid, Prions, and Other Protein Aggregates by Anonim Pdf

The ability of polypeptides to form alternatively folded, polymeric structures such as amyloids and related aggregates is being increasingly recognized as a major new frontier in protein research. This new volume of Methods in Enzymology along with Part C (volume 413) on Amyloid, Prions and other Protein Aggregates continue in the tradition of the first volume (309) in containing detailed protocols and methodological insights, provided by leaders in the field, into the latest methods for investigating the structures, mechanisms of formation, and biological activities of this important class of protein assemblies. Presents detailed protocols Includes troubleshooting tips Provides coverage on structural biology, computational methods, and biology

Author : Martin Zacharias
Publisher : World Scientific
Page : 401 pages
File Size : 53,9 Mb
Release : 2010
Category : Science
ISBN : 9781848163393

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Protein-protein Complexes by Martin Zacharias Pdf

Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.