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Computer Simulations Of Aggregation Of Proteins And Peptides
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Book Synopsis Computer Simulations of Aggregation of Proteins and Peptides by : Mai Suan Li
Download or read book Computer Simulations of Aggregation of Proteins and Peptides written by Mai Suan Li and published by Humana. This book was released on 2022-02-16 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein Folding, Misfolding and Aggregation by : Victor Muñoz
Download or read book Protein Folding, Misfolding and Aggregation written by Victor Muñoz and published by Royal Society of Chemistry. This book was released on 2008-06-24 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Investigating the Molecular Basis of Protein Aggregation and Alzheimer's Disease with Multi-scale Computer Simulations by : Mary Griffin Krone
Download or read book Investigating the Molecular Basis of Protein Aggregation and Alzheimer's Disease with Multi-scale Computer Simulations written by Mary Griffin Krone and published by ProQuest. This book was released on 2007 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of disorders are associated with the deposition of a variety insoluble protein aggregates. A great deal of evidence has led to the hypothesis that there exists a commonality between the aggregation processes of this diverse body of proteins and peptides. Understanding the universally applicable factors which influence the formation and stability of protein aggregates will provide a better understanding of the diseases to which they lead. To this end, we study several intrinsic and environmental factors which influence protein aggregation, including the role of water, the amount of frustration inherent in the individual proteins, confinement, and protein-surface interactions.
Book Synopsis Computer Simulations of Protein Folding and Aggregation by :
Download or read book Computer Simulations of Protein Folding and Aggregation written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computer Simulations of Protein Structures and Interactions by : Serafin Fraga
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer. This book was released on 1995-08-18 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Book Synopsis Computer Simulations of Protein Folding and Aggregation by : Hung Duc Nguyen
Download or read book Computer Simulations of Protein Folding and Aggregation written by Hung Duc Nguyen and published by . This book was released on 2004 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: Keywords: fibril formation, protein folding, protein aggregation, polyalanine, amyloid, computer simulation, molecular dynamics.
Book Synopsis Computer Simulations of Peptides and Proteins by : Zrinka Gattin
Download or read book Computer Simulations of Peptides and Proteins written by Zrinka Gattin and published by . This book was released on 2008 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Simulation of Polyglutamine Aggregation With An Intermediate Resolution Protein Model by :
Download or read book Simulation of Polyglutamine Aggregation With An Intermediate Resolution Protein Model written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The pathological manifestation of nine hereditary neurodegenerative diseases including Huntington's disease is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. The molecular level mechanisms by which these proteins aggregate are still unclear. In an effort to shed light on this important phenomenon, we are investigating the aggregation of model fibril-forming peptides using molecular-level computer simulation. A simplified model of polyglutamine, the protein that is known to form fibrils (ordered aggregates of proteins in beta-sheet conformations) in the brains of victims of Huntington's disease, has been developed. This model accounts for the most important types of intra- and inter-molecular interactions - hydrogen bonding and hydrophobic interactions - while allowing the folding process to be simulated in a reasonable time frame. The model utilizes discontinuous potentials such as hard spheres and square wells in order to take advantage of discontinuous molecular dynamics (DMD), a fast simulation technique that is very computationally efficient. DMD is used to examine the folding and aggregation of systems of model polyglutamine peptides ranging in size from isolated peptides to 96 peptides. In our simulations we observe the spontaneous formation of aggregates and annular structures that are made up of beta sheets starting from random configurations of random coils. The effect of chain length on the behavior of our model peptides was examined by simulating the folding of isolated polyglutamine peptides 16, 32, and 48 residues long and the folding and aggregation of systems of twenty-four model polyglutamine peptides 16, 32, 36, 40, and 48 residues long. In our multi-peptide simulations we observed that the optimal temperature for the formation of beta sheets increases with chain length up to 36 glutamine residues but not beyond. Our finding of this critical chain length of 36.
Book Synopsis Protein Aggregation, Membrane Curvature and Tubular Invagination by : Weria Pezeshkian
Download or read book Protein Aggregation, Membrane Curvature and Tubular Invagination written by Weria Pezeshkian and published by . This book was released on 2014 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Long Time Scale Computer Simulations of Proteins by : Peter Eastman
Download or read book Long Time Scale Computer Simulations of Proteins written by Peter Eastman and published by . This book was released on 2000 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Conformations of Disordered Peptides by :
Download or read book Conformations of Disordered Peptides written by and published by . This book was released on 2014 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: The unstructured conformations of intrinsically disordered proteins provide a challenge to researchers hoping to understand protein structures and diseases such as Type II diabetes. These proteins adopt a diverse set of structures, interconverting on timescales difficult for traditional techniques such as NMR and X-ray crystallography to resolve. Computer simulations provide a technique capable of understanding the structures these peptides take, their dynamics, and how they function. Through iteratively providing computational predictions and testing our hypotheses with experiments, we are able to gain key insights into topics such as protein aggregation and new biomaterials. First, the peptide involved in Type II diabetes, amylin is examined using bias exchange metadynamics simulations. These simulations are used to probe the conformations amylin takes in solution and near lipid membranes. The impact of force field choice on the secondary structures formed is predicted, showing that qualitatively different results are obtained for the same system depending on which force field is used. With these insights, we then study how amylin behaves near lipid membranes. Next we examine how the chirality of peptide backbones can be used to tune the properties of new biomaterials. Coacervates are a liquid-liquid phase equilibria that can be formed from poly(glutamic acid) and poly(lysine). By changing the ratios of L to D amino acids in the backbone, experiments have shown that a coacervate or precipitate phase can form. Using replica exchange solute scaling and other methods, the effect of backbone chirality on the secondary structures the peptides adopt is determined. We show that the change from L to D chirality introduces a kink in the peptide backbone, which disrupts [beta]-sheets and prevents the formation of precipitates.
Book Synopsis Computer Simulations of Protein-peptide Complexes Using the Myosin Light Chain Protein as a Model by : Assaf Ganoth
Download or read book Computer Simulations of Protein-peptide Complexes Using the Myosin Light Chain Protein as a Model written by Assaf Ganoth and published by . This book was released on 2006 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Amyloid, Prions, and Other Protein Aggregates, Part B by :
Download or read book Amyloid, Prions, and Other Protein Aggregates, Part B written by and published by Elsevier. This book was released on 2006-10-06 with total page 445 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly by :
Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-18 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Book Synopsis Biophysics And Biochemistry Of Protein Aggregation: Experimental And Theoretical Studies On Folding, Misfolding, And Self-assembly Of Amyloidogenic Peptides by : Jian-min Yuan
Download or read book 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 published by World Scientific. This book was released on 2017-06-02 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein Self-Assembly by : Jennifer J. McManus
Download or read book Protein Self-Assembly written by Jennifer J. McManus and published by Humana. This book was released on 2020-08-08 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. 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. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.
Book Synopsis Advances in Protein and Peptide Sciences by : Ben M. Dunn
Download or read book Advances in Protein and Peptide Sciences written by Ben M. Dunn and published by Bentham Science Publishers. This book was released on 2013-10-30 with total page 911 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein and Peptide Sciences is a book series focused on leading-edge research on the structure, physical properties, and functions of proteins and peptides. The series presents highly cited contributions first published in the journal Current Protein and Peptide Science. Authors of these contributions have updated their work with new experimental data and references following their initial research. Each volume highlights a number of important topics in current research in the field of protein and peptide chemistry and molecular biology, including membrane proteins and their interactions with ligands, computational methods, and proteins in disease and biotechnology.
