Download or read book Monte Carlo Simulations of the Thermodynamics of Folding and Denaturation Transitions for Simple Model Proteins written by Eamonn M. O'Toole and published by . This book was released on 1993 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Statistical Thermodynamics of Protein Folding written by Ming-Hong Hao and published by . This book was released on 1994 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Lattice Models of Protein Folding Dynamics and Thermodynamics written by Andrzej Koliński and published by Landes Bioscience. This book was released on 1996 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Extended Ensemble Monte Carlo Simulations of Coarse grained Protein Models written by Alfred Christopher Kaushal Farris and published by . This book was released on 2019 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work, we compare and contrast protein folding behavior in various coarse-grained, "reduced-alphabet" amino acid models, both on- and off-lattice, in an attempt to illuminate the effects of certain interaction parameters on the folding process, as well as to uncover the impact of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods -- Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar (HP), hydrophobic-"neutral"--Polar (H0P), and semi-flexible H0P model frameworks. Through analysis of specific heat curves in combination with structural observables, we paint a picture of the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature -- the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining, and that, surprisingly, the lattice models yield results that are more similar to those found in experiments.

Download or read book Monte Carlo Simulations of Supported Biomembranes and Protein Folding written by Kristian Dimitrievski and published by . This book was released on 2006 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Folding Evolution and Design written by Eugene I. Shakhnovich and published by IOS Press. This book was released on 2001 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text presents the results of broad, interdisciplinary effort to study proteins in physical and evolutionary perpective. Among authors are physicists, computational, chemists, crystallographers and evolutionary biologists. Experimental and theoretical developments from molecules to cells are presented, providing a broad picture of modern biophysical chemistry.

Download or read book Lectures on Statistical Physics and Protein Folding written by Kerson Huang and published by World Scientific. This book was released on 2005 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces an approach to protein folding from the point of view of kinetic theory. There is an abundance of data on protein folding, but few proposals are available on the mechanism driving the process. Here, presented for the first time, are suggestion on possible research directions, as developed by the author in collaboration with C. C. Lin. The first half of this invaluable book contains a concise but relatively complete review of relevant topics in statistical mechanics and kinetic theory. It includes standard topics such as thermodynamics, the Maxwell-Boltzmann distribution, and ensemble theory. Special discussions include the dynamics of phase transitions, and Brownian motion as an illustration of stochastic processes. The second half develops topics in molecular biology and protein structure, with a view to discovering mechanisms underlying protein folding. Attention is focused on the energy flow through the protein in its folded state. A mathematical model, based on the Brownian motion of coupled harmonic oscillators, is worked out in the appendix.

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.

Download or read book Protein Actions Principles and Modeling written by Ivet Bahar and published by Garland Science. This book was released on 2017-02-14 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.

Download or read book Protein Folding Dynamics written by Marcos Rubén Betancourt and published by . This book was released on 1995 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2007 with total page 854 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Monte Carlo Simulations of Protein Folding written by Aaron Reuven Dinner and published by . This book was released on 1999 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Simulation of the Interaction Between Proteins and a Charge nanopartterned i e Nanopatterned Surface written by Miwako Nakahara and published by . This book was released on 2005 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Monte Carlo Simulations of the Thermal Denaturation Transition of Model DNA Chains in Solution written by Juan C. Araque and published by . This book was released on 2006 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Folding written by Victor Muñoz and published by Humana. This book was released on 2021-11-30 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides comprehensive protocols on experimental and computational methods that are used to study probe protein folding reactions and mechanisms. Chapters divided into five parts detail protein engineering, protein chemistry, experimental approaches to investigate the thermodynamics and kinetics of protein folding transitions, probe protein folding at the single molecule, analysis and interpretation of computer simulations, procedures and tools for the prediction of protein folding properties. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Folding: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations

Download or read book Mathematical Modeling for Genes to Collective Cell Dynamics written by Tetsuji Tokihiro and published by Springer Nature. This book was released on 2022-02-23 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the dynamics of biological cells and their mathematical modeling. The topics cover the dynamics of RNA polymerases in transcription, construction of vascular networks in angiogenesis, and synchronization of cardiomyocytes. Statistical analysis of single cell dynamics and classification of proteins by mathematical modeling are also presented. The book provides the most up-to-date information on both experimental results and mathematical models that can be used to analyze cellular dynamics. Novel experimental results and approaches to understand them will be appealing to the readers. Each chapter contains 1) an introductory description of the phenomenon, 2) explanations about the mathematical technique to analyze it, 3) new experimental results, 4) mathematical modeling and its application to the phenomenon. Elementary introductions for the biological phenomenon and mathematical approach to them are especially useful for beginners. The importance of collaboration between mathematics and biological sciences has been increasing and providing new outcomes. This book gives good examples of the fruitful collaboration between mathematics and biological sciences.