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A Three Dimensional Animation System For Protein Folding Simulation
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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:
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.
Book Synopsis International Journal of Bioinformatics Research and Applications by :
Download or read book International Journal of Bioinformatics Research and Applications written by and published by . This book was released on 2006 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book ICOT Journal written by and published by . This book was released on 1994 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
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.
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.
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.
Download or read book Proceedings written by and published by . This book was released on 2005 with total page 782 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
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.
Book Synopsis Masters Theses in the Pure and Applied Sciences by : Wade H. Shafer
Download or read book Masters Theses in the Pure and Applied Sciences written by Wade H. Shafer and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Masters Theses in the Pure and Applied Sciences was first conceived, published, and disseminated by the Center for Information and Numerical Data Analysis and Synthesis (CINDAS)* at Purdue University in 1957, starting its coverage of theses with the academic year 1955. Beginning with Volume 13, the printing and dis semination phases of the activity were transferred to University Microfilms/Xerox of Ann Arbor, Michigan, with the thought that such an arrangement would be more beneficial to the academic and general scientific and technical community. After five years of this joint undertaking we had concluded that it was in the interest of all concerned if the printing and distribution of the volumes were handled by an international publishing house to assure improved service and broader dissemination. Hence, starting with Volume 18, Masters Theses in the Pure and Applied Sciences has been disseminated on a worldwide basis by Plenum Publishing Corporation of New York, and in the same year the coverage was broadened to include Canadian universities. All back issues can also be ordered from Plenum. We have reported in Volume 39 (thesis year 1994) a total of 13,953 thesis titles from 21 Canadian and 159 United States universities. We are sure that this broader base for these titles reported will greatly enhance the value of this impor tant annual reference work. While Volume 39 reports theses submitted in 1994, on occasion, certain uni versities do report theses submitted in previous years but not reported at the time.
Book Synopsis Biomedical Index to PHS-supported Research by :
Download or read book Biomedical Index to PHS-supported Research written by and published by . This book was released on 1990 with total page 866 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Folding Dynamics and Stability by : Prakash Saudagar
Download or read book Protein Folding Dynamics and Stability written by Prakash Saudagar and published by Springer Nature. This book was released on 2023-05-27 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.
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.
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.
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.
