A Three-dimensional Animation System for Protein Folding Simulation

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ISBN 13 :
Total Pages : 10 pages
Book Rating : 4.:/5 (123 download)

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Book Synopsis A Three-dimensional Animation System for Protein Folding Simulation by : Shin Sedai Konpyūta Gijutsu Kaihatsu Kikō (Japan)

Download or read book A Three-dimensional Animation System for Protein Folding Simulation written by Shin Sedai Konpyūta Gijutsu Kaihatsu Kikō (Japan) and published by . This book was released on 1993 with total page 10 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Protein Folding

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Publisher : Springer
ISBN 13 : 331900882X
Total Pages : 63 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Protein Folding by : Cláudio M. Gomes

Download or read book Protein Folding written by Cláudio M. Gomes and published by Springer. This book was released on 2019-02-25 with total page 63 pages. Available in PDF, EPUB and Kindle. Book excerpt: This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.

Modeling and Simulation of Protein Folding

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Publisher : Cuvillier Verlag
ISBN 13 : 3736937989
Total Pages : 218 pages
Book Rating : 4.7/5 (369 download)

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Book Synopsis Modeling and Simulation of Protein Folding by : Anna Shumilina

Download or read book Modeling and Simulation of Protein Folding written by Anna Shumilina and published by Cuvillier Verlag. This book was released on 2011-06-22 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book describes a new mathematical model for intracellular protein folding and the implementation of this model in the form of a novel simulation software. Besides, the related biological, chemical, and physical background, important for understanding and rationalization of the proposed model, is outlined, and a short overview of the best-known methods for protein structure prediction and molecular modeling is given. The first chapter provides a general introduction to the problem, characterizes the chemical structure of proteins, and summarizes amino acid properties, including chirality and ionization behavior. After that, the principles of quantum mechanics and their consequences for the molecular structure are described. The discussion goes over to covalent and hydrogen bonding, as well as to electrostatic and van der Waals interactions. Further, some known facts about the three-dimensional structure of proteins and typical conformations of amino acids are outlined, followed by a quick glance at the hydrophobic effect and the interaction of charged groups with the solvent. Later on the focus is shifted to biological aspects, starting with chaperons and assisted protein folding, mentioning prions, which put into question the popular hypothesis about the global energy minimum of any native structure, and continuing with details of protein synthesis in the cell, which constituted the basis for the proposed model. The chapter finishes with a short description of experimental methods for protein structure prediction and with some information about databases for storage of known protein structures. The second chapter starts with a short overview of the knowledge-based protein structure prediction and ab initio protein folding approaches, then continues with empirical molecular mechanics force fields, typically used for molecular modeling. After that, it describes computation of atomic partial charges with a focus on the procedure of J. Gasteiger and M. Marsili, and proceeds with some models for hydrogen bonding. The chapter ends with a discussion about implicit solvation models. The third chapter describes the new modeling approach and some mathematical theory developed in relation to it. The idea of the model is to simulate a process resembling intracellular cotranslational folding. An attachment of a new residue is performed in a way that the formed peptide group is disposed in the trans conformation, and only the chain twisting about certain single bonds is allowed. Transitions with an energy increase are permitted to a limited extent. Beside the electrostatic and van der Waals interactions, the proposed model incorporates hydrogen and disulfide bonding, solvation effects, and dielectric screening at the protein surface. A general expression connecting interatomic distances and dihedral angles is derived, which resulted in a formulation of the model in the space of molecular torsion angles. Twisting forces are computed analytically and utilized for the improvement of computational efficiency the folding simulations. Besides, equations for dynamics in the space of torsion angles are derived, and a conclusion related to folding pathways is drawn. The last chapter discusses some non-technical details related to the implementation of the proposed model, including a number of developed algorithms, and the resulting simulation software. The chapter ends with a short discussion of simulation results and with an outlook. This book is aimed in the first place to biophysicists and bioinformaticians, but can be also interesting for theoretical chemists, mathematicians, and molecular biologists, since it includes a broad interdisciplinary overview accompanied by unique visualizations, which were performed with the help of the simulation software developed by the author.

Protein Folding

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Publisher : Springer
ISBN 13 : 3319125923
Total Pages : 61 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Protein Folding by : Alka Dwevedi

Download or read book Protein Folding written by Alka Dwevedi and published by Springer. This book was released on 2014-12-01 with total page 61 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book will discuss classes of proteins and their folding, as well as the involvement of bioinformatics in solving the protein folding problem. In vivo and in vitro folding mechanisms are examined, as well as the failures of in vitro folding, a mechanism helpful in understanding disease caused by misfolding. The role of energy landscapes is also discussed and the computational approaches to these landscapes.

The Protein Folding Problem

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Publisher : Routledge
ISBN 13 : 1000305031
Total Pages : 171 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis The Protein Folding Problem by : Donald B Wetlaufer

Download or read book The Protein Folding Problem written by Donald B Wetlaufer and published by Routledge. This book was released on 2019-06-21 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins in living systems carry out a great variety of specific functions, each of which depends on the precise three-dimensional structure of a particular protein. Proteins are synthesized in the form of a flexible polypeptide chain that is capable of assuming a vast number of configurations; the transformation of this chain into a specific, relatively rigid three-dimensional structure is called folding--a remarkable process of self-organization. It is known that the amino acid sequences of some proteins have sufficient information to determine their three-dimensional structures. There are other proteins whose folding requires additional information beyond that found in the sequence of the mature protein. This book introduces the central problem of folding mechanisms as well as a number of other closely related issues. This book is neither a textbook nor a treatise. Rather, it is an attempt by several investigators to convey the excitement and challenges of those aspects of the folding problem in which they are actively engaged. The contributors give brief introductions to protein folding from the perspectives of molecular architecture, stability and dynamics, phage genetics, DNA exons, general physiology, and natural selection. They point out emerging new directions, including the suggestion of a class of diseases that result from protein folding defects.

Understanding Protein Folding Using Molecular Dynamics Simulation

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Publisher : LAP Lambert Academic Publishing
ISBN 13 : 9783659177644
Total Pages : 280 pages
Book Rating : 4.1/5 (776 download)

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Book Synopsis Understanding Protein Folding Using Molecular Dynamics Simulation by : Sunita Patel

Download or read book Understanding Protein Folding Using Molecular Dynamics Simulation written by Sunita Patel and published by LAP Lambert Academic Publishing. This book was released on 2013 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: The way a protein fold into a three dimensional structure and perform its function is still remains as protein folding puzzle. In the present work, we attempt to understand how the information encoded in the primary sequence of a protein gets translated into a three dimensional structure is studied on the peptide models from various proteins using molecular dynamics simulation. We also attempt to understand the nature of unfolded state under physiological conditions. On the whole these two aspects are emphasized in this book.

A Motion Planning Approach to Protein Folding

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ISBN 13 :
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Book Synopsis A Motion Planning Approach to Protein Folding by : Guang Song

Download or read book A Motion Planning Approach to Protein Folding written by Guang Song and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is considered to be one of the grand challenge problems in biology. Protein folding refers to how a protein's amino acid sequence, under certain physiological conditions, folds into a stable close-packed three-dimensional structure known as the native state. There are two major problems in protein folding. One, usually called protein structure prediction, is to predict the structure of the protein's native state given only the amino acid sequence. Another important and strongly related problem, often called protein folding, is to study how the amino acid sequence dynamically transitions from an unstructured state to the native state. In this dissertation, we concentrate on the second problem. There are several approaches that have been applied to the protein folding problem, including molecular dynamics, Monte Carlo methods, statistical mechanical models, and lattice models. However, most of these approaches suffer from either overly-detailed simulations, requiring impractical computation times, or overly-simplified models, resulting in unrealistic solutions. In this work, we present a novel motion planning based framework for studying protein folding. We describe how it can be used to approximately map a protein's energy landscape, and then discuss how to find approximate folding pathways and kinetics on this approximate energy landscape. In particular, our technique can produce potential energy landscapes, free energy landscapes, and many folding pathways all from a single roadmap. The roadmap can be computed in a few hours on a desktop PC using a coarse potential energy function. In addition, our motion planning based approach is the first simulation method that enables the study of protein folding kinetics at a level of detail that is appropriate (i.e., not too detailed or too coarse) for capturing possible 2-state and 3-state folding kinetics that may coexist in one protein. Indeed, the unique ability of our method to produce large sets of unrelated folding pathways may potentially provide crucial insight into some aspects of folding kinetics that are not available to other theoretical techniques.

Local Search-based Protein Folding Simulations

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ISBN 13 :
Total Pages : 340 pages
Book Rating : 4.:/5 (757 download)

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Book Synopsis Local Search-based Protein Folding Simulations by : Leonidas Kapsokalyvas

Download or read book Local Search-based Protein Folding Simulations written by Leonidas Kapsokalyvas and published by . This book was released on 2011 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract. Protein folding is the physical process in which a protein acquires its structure that allows it to perform a specific biological task. Proteins fold spon-taneously into three-dimensional structures of minimum energy when found in the appropriate environment. The study of this phenomenon is often facilitated through local search-based computer simulations in which the energy of a protein is mini¬mized. This thesis is concerned with local search methods for protein folding simulations in rectangular and triangular lattice models as well as in a simplified coarse-grained off-lattice model. The aim of those simulations is on the one hand protein struc¬ture prediction and on the other hand energy landscape analysis. Lattice models are often useful in the study of protein folding, since they allow exact enumeration of solutions, easy identification of local minima and paths leading to them. The challenge for local search-based methods in lattice model simulations is to efficiently sample an exponentially large search space. In that respect this thesis contributes a method to reduce the search space in rectangular lattices, which is adapted into specific neighborhood relations and is used in local search methods. This method is based on restricting search to a reduced subspace of protein structures, free from some special symmetrical versions of the same structure. The thesis also contributes a novel local search method for protein structure prediction, namely a population based local search. The novel local search method can be used to gather local min¬ima of the underlying energy landscape. The method outperforms the state-of-the-art method tested for the specific set of benchmarks in the cubic lattice and the MJ(Miyazawa-Jernigan) energy model. The survey of the energy landscape in the latter model reveals that the energy of local minima follows a Gaussian-like distri¬bution.

Simulating Temperature Jumps for Protein Folding Studies

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (663 download)

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Book Synopsis Simulating Temperature Jumps for Protein Folding Studies by : Seonah Kim

Download or read book Simulating Temperature Jumps for Protein Folding Studies written by Seonah Kim and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Protein folding is described as a dynamic process of an ensemble of molecules reaching well-defined three dimensional structures to achieve biological activity from linear amino acids sequences. Many human diseases result from protein misfolding or aggregation. Enormous effort has been made both experimentally and theoretically for nearly 40 years to explain the basic principle and mechanism of protein folding and unfolding. Nonetheless, many of them are still unknown or incompletely understood, mainly due to the complexity of the systems and the fast folding time scale. Experimental and theoretical approaches are complementary with each other for the protein folding studies and hence, combination of the two is required to have better understanding. One of the most popular experimental methods for the protein folding studies is laser-induced temperature-jump (T-jump), because it has nanosecond resolution. In the first project, the T-jump on the polyalanine peptides (Ala20) was simulated as a proof-of-principle system to mimic the experimental measurements. Replica exchange molecular dynamics (REMD) were performed to obtain equilibrated ensembles as a proper conformational sampling, which was combined with multiplexed molecular dynamics to extract kinetic properties in line with experiments. In the second project, the same methodology used in the first project was applied to real proteins. Effect of frictional coefficient in the solvent model was approximated using Langevin dynamics. Computationall results on the two related 14-residue peptides were chosen and compared with experimental results. A ratio of relaxation time of the two peptides was determined by calculated Circular Dichroism (CD) spectra by a factor of ~1.2, while the experimental results were ~1.1.

The Protein Folding Problem and Tertiary Structure Prediction

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Publisher : Birkhäuser
ISBN 13 : 9781468468328
Total Pages : 581 pages
Book Rating : 4.4/5 (683 download)

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Book Synopsis The Protein Folding Problem and Tertiary Structure Prediction by : Kenneth Merz

Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth Merz and published by Birkhäuser. This book was released on 2012-10-19 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Understanding the Determining Factors and Their Cooperative Effects on Protein Folding

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ISBN 13 :
Total Pages : pages
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Book Synopsis Understanding the Determining Factors and Their Cooperative Effects on Protein Folding by : Yue Li

Download or read book Understanding the Determining Factors and Their Cooperative Effects on Protein Folding written by Yue Li and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Protein is a linear chain of amino acids bonded by peptide bonds. Protein plays a vital role in almost every biological process. For most proteins, they need to fold into a stable 3D structure (native state) in order to function properly. This process that proteins fold from the sequence of amino acids to the 3D structure is known as protein folding. The relations among protein sequence, structure and function have been studied for many years in lab by expensive experimental methods such as X-ray crystallography and NMR spectroscopy. The emerging high performance microprocessors enable efficient and accurate protein structure simulation. Despite extensive studies previously, the factors behind the protein folding and their cooperative effects are still not completely understood. This dissertation presents the methods and results about investigating the determining factors for protein folding and their cooperative effects. We start with a simplified protein folding model, three-dimensional hydrophobic-polar (HP) model which only care about the hydrophobic interaction because it is believed that the hydrophobic interaction between residues is the driving force for protein folding. Although HP model is simple, it is useful enough to provide us a platform to measure the stability of protein which will eventually benefit us in the design of protein sequences. The funnel-shape energy landscape theory [2][3] states that a protein can fold into its specific three-dimensional structure through multiple pathways. There are many local minima during the process of folding. Protein can be trapped in these local minima temporarily, but eventually it will be guided towards the native state. Therefore, energy landscape entropy (ELE) is proposed to measure the foldability of a protein sequence. Based on our experimental results, the proportion of hydrophobic residues which is defined as hydrophobic content (HC) plays a determining role in the foldability of a protein sequence. A specific range of HC is the key for HP sequences to maintain the stability. To compare our simulation results with real protein sequences, we probed the proportion of hydrophobic residues values in a set of non-homologous globular proteins. We also reviewed the HC values of sequences of intrinsically disordered proteins (IDPs) from DisProt database. We then compared the hydrophobic contents between globular proteins and intrinsically disordered proteins (IDPs). We found that IDPs tend to occupy the lower range in the HC spectrum which matches the fact that IDPs have marginally stable states in their energy landscapes. The research on the proportion of hydrophobic residues shed a light on the protein design because it will prune the astronomical space of protein sequences. Previously, we have to enumerate every possible protein sequence in order to design a protein with specified function. With the aid of the knowledge about the proportion of hydrophobic residues, we can exclude a large number of redundant sequences whose proportion of hydrophobic residues is not eligible. However, the protein folding is a complicated process affected by multiple factors. In order to investigate these factors and their cooperative effects, an optimized energy function on a more realistic protein model is required. The quality of an energy function is the key of the success in protein structure prediction. Optimizing an energy function is a non-trivial problem in protein structure prediction. We propose to optimize the weights associated with energy terms by using the near native structures (NNS). The near native structure (NNS) is defined as the set of conformation whose side-chain dihedral angles are within a certain degree away from the native structure in this dissertation. The near native structure provides us an opportunity to assess the quality of an energy function. Correspondingly, the probability of the near native structure for a single type of residue is proposed. The optimized energy function will minimize the probability of the near native structure. The results indicate that our method invariably improve the average probability of the near native structure. We also find the similarity in the topology of side-chain infers the similar weights. However, there is no general configuration of weights for all twenty types of amino acids under current energy function. It is obvious that not all the determining factors are integrated into the current model consisting of only five energy terms. The current energy function is too coarse-grained to reflect the cooperative effects of all determining factors. When scientists design the energy function for protein structure prediction, it should be noted that the energy function should be fine-grained enough to disclose all the determining factors behind protein folding.

A Physically-based Simulation Approach to Three-dimensional Computer Animation

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Publisher :
ISBN 13 :
Total Pages : 534 pages
Book Rating : 4.:/5 (213 download)

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Book Synopsis A Physically-based Simulation Approach to Three-dimensional Computer Animation by : Craig Bernreuter Caldwell

Download or read book A Physically-based Simulation Approach to Three-dimensional Computer Animation written by Craig Bernreuter Caldwell and published by . This book was released on 1989 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Modeling and Predicting Co-translational Protein Folding with Chemical Kinetic and Molecular Dynamic Simulations

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ISBN 13 :
Total Pages : pages
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Book Synopsis Modeling and Predicting Co-translational Protein Folding with Chemical Kinetic and Molecular Dynamic Simulations by : Daniel Nissley

Download or read book Modeling and Predicting Co-translational Protein Folding with Chemical Kinetic and Molecular Dynamic Simulations written by Daniel Nissley and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are linear polymers of amino acids that perform myriad functions within living cells. Most proteins must form a specific three-dimensional structure, often referred to as the native state, in order to perform their biological function. The process of reaching the native state is termed protein folding. It is often assumed that thermodynamics alone determines the specific conformation of the native state of a protein, meaning that its structure is determined by the amino-acid sequence alone. Within living cells, however, proteins are translated based on mRNA templates by the ribosome in a distinctly out-of-equilibrium fashion. The non-equilibrium nature of translation means that kinetics can trump thermodynamics in determining the conformation of a protein, and recent experiments indicate that seemingly small changes to the kinetics of translation can radically alter protein structure and function and even lead to disease. One way in which the speed of translation can be perturbed is through synonymous codon mutations, which change the rate of translation but not the primary sequence of the nascent protein that is produced. Understanding how the non-equilibrium nature of protein synthesis influences the likelihood that a given protein will correctly fold and function is therefore critical to understanding protein biogenesis.This thesis contains four theoretical and computational studies of co-translational protein folding and its influence on protein conformations after synthesis is complete. The state of the experimental and computational literature is summarized in Chapter 1. In Chapter 2 I describe a chemical kinetic model that is able to accurately predict experimental co-translational folding probabilities for the first time. This chemical kinetic model is used to make the novel prediction that some yeast proteins which typically fold post-translationally can be made to fold co-translationally by recoding their mRNA sequences to contain the slowest-translating synonymous codon at each codon position. This chemical kinetic model is general, in principle, for all proteins and all organisms. The fluorescent technique FRET has recently been used to monitor protein folding on the ribosome both in vitro and in vivo. One disadvantage of such fluorescent techniques is that they produce a single value per time point, providing minimal structural information. In Chapter 3, I present results from low-friction, coarse-grain Langevin dynamics simulations that elucidate the structural origins of FRET measurements on the ribosome. These simulations are in strong agreement with experimental time series and reveal the underlying co-translational folding trajectory at a spatial resolution of 3.8 . I also show that the alternative hypothesis that nascent chain compaction occurs due to collapse as is expected for a polymer in poor solvent is not consistent with the experimental data. Dimensional collapse, however, could not be ruled out. I therefore suggest alternative dye positions that could be used to differentiate domain folding and domain dimensional collapse in future experiments.Chapter 4 of this thesis presents the hypothesis that the pathogenesis of Huntingtons Disease is, at least in part, due to the dysfunction of a co-translational process. The genetic cause of Huntingtons Disease is the expansion of a poly-glutamine region in Exon 1 of the HTT gene. Individuals with 35 or more CAG codons (which encode the amino acid glutamine) in their HTT gene will suffer disease symptom onset within a typical human lifespan. The age of symptom onset decreases linearly as the number CAG codons increases beyond 35. Based on strong circumstantial experimental evidence and a simple kinetic model, I argue that the expansion of the CAG codon region in the transcript leads to an increase in the speed of translation at a key time during the synthesis of huntingtin protein that leads to its misprocessing and the onset of disease symptoms. I go on to propose experiments to test this hypothesis. In Chapter 5 I describe high-throughput simulations of the translation elongation, translation termination, and post-translational dynamics of a representative subset of the E. coli cytosolic proteome. I find that roughly one in four proteins is kinetically trapped for as long as 3 minutes after the completion of protein synthesis.Finally, in Chapter 6 I summarize the conclusions that can be drawn from, and the future directions related to, my work. One obvious future goal is the extension of my simulations of multi-domain E. coli proteins to the study of how domain interfaces influence protein folding. That is, do domains fold independently or do they rely upon one another? My E. coli proteome data set also includes diverse information about translation termination kinetics, and preliminary simulations reveal that electrostatic effects seem to largely determine its timescales. In summary, the results presented in this thesis advance understanding of co-translational protein folding and the influence translation kinetics can have on protein conformations.

A 3D Animation System for Functional Simulation, Visualization, and Control of Dynamic Processes Based on Parallel Rewriting

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ISBN 13 :
Total Pages : 257 pages
Book Rating : 4.:/5 (853 download)

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Book Synopsis A 3D Animation System for Functional Simulation, Visualization, and Control of Dynamic Processes Based on Parallel Rewriting by : Hansrudi Noser

Download or read book A 3D Animation System for Functional Simulation, Visualization, and Control of Dynamic Processes Based on Parallel Rewriting written by Hansrudi Noser and published by . This book was released on 2004 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computer Simulations of Protein Folding and Aggregation

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ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (656 download)

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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.

Does Protein Folding Exhibit Self-organized Criticality?

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ISBN 13 :
Total Pages : 74 pages
Book Rating : 4.:/5 (922 download)

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Book Synopsis Does Protein Folding Exhibit Self-organized Criticality? by :

Download or read book Does Protein Folding Exhibit Self-organized Criticality? written by and published by . This book was released on 2014 with total page 74 pages. Available in PDF, EPUB and Kindle. Book excerpt:

In Silico

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Publisher : Morgan Kaufmann
ISBN 13 : 9780123736550
Total Pages : 622 pages
Book Rating : 4.7/5 (365 download)

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Book Synopsis In Silico by : Jason Sharpe

Download or read book In Silico written by Jason Sharpe and published by Morgan Kaufmann. This book was released on 2008 with total page 622 pages. Available in PDF, EPUB and Kindle. Book excerpt: Preface - Who is this book for? Why Maya? What the book offers Acknowledgments Contact us; Part 1 - Setting the stage, Chapter 1 - Introduction the challenge wetware for seeing visualization in science organizational hierarchy - keys to biology in vivo and in silico - Enter maya endless possibilities references; Chapter 2 - Computers and the organism introduction information and process language and program high and low Interpret or compile? The backus watershed stored programs conditional control, the computed organism, the computational organism OOPS and agents summary references; Chapter 3 - Animating biology introduction, animation and film perception. Part 2 - A foundation in maya, Chapter 4 - Maya basics, getting started, how maya works, Maya's user interface (UI) summary; Chapter 5 - Modeling geometry, introduction NURBS modeling Tutorial; 05.01 - NURBS primitive modeling Tutorial; 05.02 - Deform the sphere using components tutorial; 05.03 - Make and deform a polygon primitive tutorial; 05.04 - Construction history tutorial; 02.05 Create a NURBS, fiber. Summary References. Chapter 6 - Animation, introduction animation tutorial; 06.01 - A keyframe animation tutorial; 06.02 - A simple procedural animation; Chapter 7 - Dynamics introduction, The dynamics module tutorial; 07.01 - Rigid body dynamics tutorial; 07.02 - Particles in a container tutorial; 07.03 - Create a playblast summary; Chapter 8 - Shading, Introduction the render menu set shading 209 tutorial; 08.01 - Shading; Chapter 9 - Cameras maya cameras tutorial; 09.01 - A camera on hemoglobin; Chapter 10 - Lighting Lighting 253 tutorial; 10.01 - Lighting the hemoglobin scene; Chapter 11 - Action! maya rendering, rendering Advanced, rendering techniques with the mental ray for Maya renderer tutorial; 11.01 - Batch rendering tutorial; 11.02 - Playback using fcheck, summary; Chapter 12 - MEL Scripting, Introduction the origins of MEL In a word - Scripting - getting started, MEL syntax Values, Variables, mathematical and logical expressions, the MEL command Attributes in MEL Conditional statements loops procedures, animation expressions, putting it all together - the MEL script tutorial; 12.01 - Building a MEL script, debugging your scripts, random number generation in Maya, summary; Chapter 13 - Data input/output, introduction, translators reading and writing files with MEL, Tutorial; 13.01 - Visualizing cell migration, summary; Part 3 - Biology in silico-maya in action, Chapter 14 - Building a protein, introduction, problem overview Methods - algorithm, design, encoding the algorithm results - running the script; Chapter 15 - Self assembly, introduction, problem overview Methods - actin geometry, diffusion and reaction events, reaction rates and probabilities, algorithm design, encoding the algorithm Results - running your simulation, summary, references; Chapter 16 - Modeling a mobile cell, introduction problem overview, model definition methods - generating pseudopods, algorithm design, A cell locomotion engine, encoding the algorithm, loading the script, running the script, Summary, references; Chapter 17 - Growing an ECM scaffold, introduction, problem overview model definition methods - Algorithm design, encoding the algorithm, grow your scaffold, results - parameter effects, summary, references, Chapter 18 - Scaffold invasions - Modeling 3D populations of mobile cells, introduction, problem overview, model definition methods - model design, encoding the algorithm, running the simulation Results - Data output, summary, references; Chapter 19 - Conclusion, glossary, further reading index.