Download or read book Explicit solvent effects on protein physics written by Giovanni Salvi and published by Sudwestdeutscher Verlag Fur Hochschulschriften AG. This book was released on 2009 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding stands as one of the major interdisciplinary challenges of the last fifteen years, involving biology, chemistry, medicine and physics. In this book solvent effects, and the related hydrophobic effect, on proteins are investigated. Using a simple lattice model of proteins, in which the solvent is semi-explicitly taken into account, thermodynamical quantities can be investigated and the crucial role the solvent plays in protein folding can be demonstrated. Of particular relevance is our observation that a simple model, in which the potential energy is described in terms of the interactions between amino-acids only, does not correctly reproduce solvent effects. Approaches like this, in which solvent effects are treated implicitly, are commonly employed in many of more sophisticated models for protein folding dynamics. Our results are then of great importance as they suggest the treatment of the solvent in these models may need to be re-examined.
Download or read book Theory and Simulation of Explicit Solvent Effects on Protein Folding in Vitro and in Vivo written by Jeremy L. England and published by . This book was released on 2009 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Methods for Protein Folding Volume 120 written by Richard A. Friesner and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.
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 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 Aggregation at Solid liquid Interfaces a Monte Carlo Study with Explicit and Implicit Solvent Effects written by Rehman Fazeem and published by . This book was released on 2013 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Metropolis Monte Carlo (MC) simulations were performed with positively charged peptides in aqueous solution to study changes in peptide conformations at solid/liquid interface, and its effects on protein aggregation. Intermediate-resolution diblock model peptide, comprising of 10 units of ALA (non-polar) and LYS (polar) amino acid residues, was used for the simulations. In the first approach to modeling, solvent effects were considered explicitly. The explicit model was then used to study two peptide molecules, in helical structure, at solid/liquid interface. In order to increase the number of peptide molecules in the simulation box, with reduced computational cost, an implicit solvent model was developed with nonadditive hydrogen bonding and hydrophobic interaction potentials. The implicit model was used to simulate two peptides of helical structure at charged surfaces (to compare with the explicit model), and ten peptides of random coil structure with and without charged surfaces. The peptides were observed to always move towards the negatively charged surface and orient with residues of complimentary charge settling close to the surface, maximizing the electrostatic interactions. On reaching the surface, the peptides partially lose their secondary structure and clusters around the hydrophobic ends; this restructuring and dehydration of the peptides provides the entropic drive for adsorption and subsequent misfolding events. The 2- peptide-water-surface system in explicit model was also simulated with periodic switching of surface charge polarity, to induce a "shaking effect" in order to observe possible peptide configurational changes"--Abstract, page iii.
Download or read book Hydrogen Bond Networks written by Marie-Claire Bellisent-Funel and published by Springer. This book was released on 2014-03-14 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: The almost universal presence of water in our everyday lives and the very `common' nature of its presence and properties possibly deflects attention from the fact that it has a number of very unusual characteristics which, furthermore, are found to be extremely sensitive to physical parameters, chemical environment and other influences. Hydrogen-bonding effects, too, are not restricted to water, so it is necessary to investigate other systems as well, in order to understand the characteristics in a wider context. Hydrogen Bond Networks reflects the diversity and relevance of water in subjects ranging from the fundamentals of condensed matter physics, through aspects of chemical reactivity to structure and function in biological systems.
Download or read book Computer Simulation of Biomolecular Systems written by W.F. van Gunsteren and published by Springer Science & Business Media. This book was released on 1997-11-30 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.
Download or read book Solvent Dependent Flexibility of Proteins and Principles of Their Function written by Aleksandr Ivanovich Ki︠a︡ĭvi︠a︡ri︠a︡ĭnen and published by Springer. This book was released on 1985 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular biology has now advanced to the point where it is no longer possible to give a complete review of the available data on the conformational features of proteins. New data keep streaming in, and there is obviously an urgent need for some sort of general treatment of the subject. A systematic treatment of the large amount of data obtained by a great variety of methods on a great variety of objects must be based on the use of models; these should be as simple as possible, should conform to well-established scien tific laws, and at the same time be sufficiently flexible. The validity of the models finally arrived at is then confirmed or otherwise by testing the conclusions arrived at with their aid by means of experiment. After a suitable model has been adopted, it can be used in analyzing the experimental data. Such an analysis may result in one of three possible situations: neither the experi mental results nor their interpretation contradict the proposed model; the experimental results do not contradict the proposed model but their interpretation by the authors does; finally, both the experimental results and their interpretation may be found to be incompatible with the fundamental principles underlying the proposed model. The first situation is clearly the most desirable, and presents no difficulties.
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. - Presents a thorough overview of the latest and emerging methods and technologies for protein study - Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy - Includes computational and machine learning methods - Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Download or read book Solvation Thermodynamics written by Arieh Y. Ben-Naim and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther modynamics alone. However, solvation is inherently a molecular pro cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 based on analysis at the molecular level. During the past ten years, I have introduced several new quantities which, in my opinion, should replace the conventional measures of solvation thermodynamics. To avoid confusing the new quantities with those referred to conventionally in the literature as standard quantities of solvation, I called these "nonconventional," "generalized," and "local" standard quantities and attempted to point out the advantages of these new quantities over the conventional ones.
Download or read book Theory of Solutions written by John G. Kirkwood and published by CRC Press. This book was released on 2001-12 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Water in Biological and Chemical Processes written by Biman Bagchi and published by Cambridge University Press. This book was released on 2013-11-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.
Download or read book Physical Review written by and published by . This book was released on 2000-03 with total page 1140 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publishes papers that report results of research in statistical physics, plasmas, fluids, and related interdisciplinary topics. There are sections on (1) methods of statistical physics, (2) classical fluids, (3) liquid crystals, (4) diffusion-limited aggregation, and dendritic growth, (5) biological physics, (6) plasma physics, (7) physics of beams, (8) classical physics, including nonlinear media, and (9) computational physics.
Download or read book High Performance Computing in Science and Engineering 14 written by Wolfgang E. Nagel and published by Springer. This book was released on 2015-02-14 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the state-of-the-art in supercomputer simulation. It includes the latest findings from leading researchers using systems from the High Performance Computing Center Stuttgart (HLRS). The reports cover all fields of computational science and engineering ranging from CFD to computational physics and from chemistry to computer science with a special emphasis on industrially relevant applications. Presenting findings of one of Europe’s leading systems, this volume covers a wide variety of applications that deliver a high level of sustained performance. The book covers the main methods in high-performance computing. Its outstanding results in achieving the best performance for production codes are of particular interest for both scientists and engineers. The book comes with a wealth of color illustrations and tables of results.
Download or read book Practical Bioinformatics written by Janusz M. Bujnicki and published by Springer. This book was released on 2007-09-12 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.
