Computer Simulations Of Protein Folding And Aggregation
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Computer Simulations Of Protein Folding And Aggregation
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Author : Hung Duc Nguyen
language : en
Publisher:
Release Date : 2004
Computer Simulations Of Protein Folding And Aggregation written by Hung Duc Nguyen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Keywords: fibril formation, protein folding, protein aggregation, polyalanine, amyloid, computer simulation, molecular dynamics.
Protein Folding Misfolding And Aggregation
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Author : Victor Muñoz
language : en
Publisher: Royal Society of Chemistry
Release Date : 2008
Protein Folding Misfolding And Aggregation written by Victor Muñoz and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.
Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods h.
Computer Simulations Of Protein Folding And Aggregation
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Author :
language : en
Publisher:
Release Date : 2004
Computer Simulations Of Protein Folding And Aggregation written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Computer simulation is used to study the competition between protein folding and aggregation, especially the formation of ordered structures that are also known as amyloid fibrils. Employing simplified protein models, we simulate multi-protein systems at a greater level of detail than has previously been possible, probe the fundamental physics that govern protein folding and aggregation, and explore the energetic and structural characteristics of amorphous and fibrillar protein aggregates. We first tackle the aggregation problem by using a low-resolution model called the lattice HP model developed by Lau and Dill. Dynamic Monte Carlo simulations are conducted on a system of simple, two-dimensional lattice protein molecules. We investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of the model protein molecule by simulating three renaturation methods: infinitely slow cooling, slow but finite cooling, and quenching. We find that the infinitely slow cooling method provides the highest refolding yields. We then study how the variation of protein concentration affects the refolding yield by simulating the pulse renaturation method, in which denatured proteins are slowly added to the refolding simulation box in a stepwise manner. We observe that the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods even at high packing fractions. We then investigate the folding of a polyalanine peptide with the sequence Ac-KA14K-NH2 using a novel off-lattice, intermediate-resolution protein model originally developed by Smith and Hall. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule is explored by employing the replica exchange simulation method to map out the conformational transitions as a function of temperature. We also explore the influence of solvent type on the folding process by varying the relative strength of the sid.
Protein Folding Misfolding And Aggregation
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Author : Victor Muñoz
language : en
Publisher: Royal Society of Chemistry
Release Date : 2008-06-24
Protein Folding Misfolding And Aggregation written by Victor Muñoz and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-06-24 with Science categories.
Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods have evolved to permit resolving fast processes of folding reactions and visualizing single molecules during folding. The findings from these novel experiments and detailed computer simulations have confirmed the main predictions of analytical theory of protein folding. In summary, protein folding research has finally acquired the status of a truly quantitative science, paving the way for more exciting developments in the near future. This unique book covers all the modern approaches and the many advances experienced in the field during the last 10 years. There is also much emphasis on computational methods and studies of protein aggregation which have really flourished in the last decade. It includes chapters in the areas that have witnessed major developments and are written by top experts including:computer simulations of folding, fast folding, single molecule spectroscopy, protein design, aggregation studies (both computational and experimental). Readers will obtain a unique perspective of the problems faced in the biophysical study of protein conformational behaviour in aqueous solution and how these problems are being solved with a multidisciplinary approach that combines theory, experiment and computer simulations. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches is essential reading for graduate students actively involved in protein folding research, other scientists interested in the recent progress of the field and instructors revamping the protein folding section of their biochemistry and biophysics courses.
Computer Simulations Of Aggregation Of Proteins And Peptides
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Author : Mai Suan Li
language : en
Publisher: Humana
Release Date : 2022-02-16
Computer Simulations Of Aggregation Of Proteins And Peptides written by Mai Suan Li and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-16 with Science categories.
This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer’s, Parkinson’s, and preeclampsia. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.
Computational Approaches For Understanding Dynamical Systems Protein Folding And Assembly
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Author :
language : en
Publisher: Academic Press
Release Date : 2020-03-04
Computational Approaches For Understanding Dynamical Systems Protein Folding And Assembly 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 2020-03-04 with Science categories.
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more.
Biophysics And Biochemistry Of Protein Aggregation Experimental And Theoretical Studies On Folding Misfolding And Self Assembly Of Amyloidogenic Peptides
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Author : Jian-min Yuan
language : en
Publisher: World Scientific
Release Date : 2017-06-02
Biophysics And Biochemistry Of Protein Aggregation Experimental And Theoretical Studies On Folding Misfolding And Self Assembly Of Amyloidogenic Peptides written by Jian-min Yuan and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-06-02 with Science categories.
This book reviews current research on the important processes involved in neurodegenerative diseases (e.g. Alzheimer's disease) and the peptides and proteins involved in the amyloidogenic processes. It covers the design and developments of anti-amyloid inhibitors, and gives readers a fundamental understanding of the underlying oligomerization and aggregation processes of these diseases from both computational and experimental points of view.
Protein Folding Mis Folding And Aggregation
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Author : Troy Lee Cellmer
language : en
Publisher:
Release Date : 2005
Protein Folding Mis Folding And Aggregation written by Troy Lee Cellmer and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with Mathematical models categories.
Protein Folding And Misfolding
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Author : Heinz Fabian
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-09-18
Protein Folding And Misfolding written by Heinz Fabian 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 2011-09-18 with Science categories.
Infrared spectroscopy is a new and innovative technology to study protein folding/misfolding events in the broad arsenal of techniques conventionally used in this field. The progress in understanding protein folding and misfolding is primarily due to the development of biophysical methods which permit to probe conformational changes with high kinetic and structural resolution. The most commonly used approaches rely on rapid mixing methods to initiate the folding event via a sudden change in solvent conditions. Traditionally, techniques such as fluorescence, circular dichroism or visible absorption are applied to probe the process. In contrast to these techniques, infrared spectroscopy came into play only very recently, and the progress made in this field up to date which now permits to probe folding events over the time scale from picoseconds to minutes has not yet been discussed in a book. The aim of this book is to provide an overview of the developments as seen by some of the main contributors to the field. The chapters are not intended to give exhaustive reviews of the literature but, instead to illustrate examples demonstrating the sort of information, which infrared techniques can provide and how this information can be extracted from the experimental data. By discussing the strengths and limitations of the infrared approaches for the investigation of folding and misfolding mechanisms this book helps the reader to evaluate whether a particular system is appropriate for studies by infrared spectroscopy and which specific advantages the techniques offer to solve specific problems.
Amyloid Prions And Other Protein Aggregates Part B
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Author :
language : en
Publisher: Elsevier
Release Date : 2006-10-06
Amyloid Prions And Other Protein Aggregates Part B 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 2006-10-06 with Science categories.
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