Explicit solvent effects on protein physics
Explicit solvent effects on protein physics

Author: Giovanni Salvi

Publisher: Sudwestdeutscher Verlag Fur Hochschulschriften AG

Published: 2009

Total Pages: 108

ISBN-13: 9783838107714

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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.

Protein Actions: Principles and Modeling
Protein Actions: Principles and Modeling

Author: Ivet Bahar

Publisher: Garland Science

Published: 2017-02-14

Total Pages: 337

ISBN-13: 1351815016

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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.

Protein Aggregation at Solid/liquid Interfaces: a Monte Carlo Study with Explicit and Implicit Solvent Effects
Protein Aggregation at Solid/liquid Interfaces: a Monte Carlo Study with Explicit and Implicit Solvent Effects

Author: Rehman Fazeem

Publisher:

Published: 2013

Total Pages: 185

ISBN-13:

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"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.

Advances in Protein Molecular and Structural Biology Methods
Advances in Protein Molecular and Structural Biology Methods

Author: Timir Tripathi

Publisher: Academic Press

Published: 2022-01-14

Total Pages: 716

ISBN-13: 0323902650

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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

Hydrogen Bond Networks
Hydrogen Bond Networks

Author: Marie-Claire Bellisent-Funel

Publisher: Springer

Published: 2014-03-14

Total Pages: 558

ISBN-13: 9789401583336

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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.

The Influence of Proteins Surface on the Ordering of Surrounded Water
The Influence of Proteins Surface on the Ordering of Surrounded Water

Author: Irena Roterman

Publisher:

Published: 2019

Total Pages: 0

ISBN-13:

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Protein folding remains not satisfactory understood process. Considering the critical importance of water for proteins and other biologically active molecules, analysis of water-protein interactions should play a central role in studies concerning the folding process and biological activity of proteins. Folding simulations should acknowledge the aqueous solvent as an active partner which determines the final conformation of a protein. In the fuzzy oil drop model (which is applied in the presented analysis), the solvent is treated as a continuum,Äîan external force field guiding the folding process. This interaction goes both ways: (1) the solvent shapes the protein and (2) the presence of a natively folded protein also alters the structure of the solvent (the structure of water has not heretofore been sufficiently studied,Äîexcept for the solid state). This work focuses on this second reverse relationship, that is, the influence of proteins upon the structuralization of water. We formulate a hypothesis which is based on the fuzzy oil drop model. The ordering of the hydrophobic core which resides inside the protein and may include local discordances is analyzed from the point of view of its external effects. In accordance to the fuzzy oil drop model, the solvent is expected to ,Äúreact,Äù to local differentiation in the properties of the molecular surface. Our hypothesis remains speculative, since experimental studies have not yet yielded sufficient evidence to either prove or disprove it. The presented analysis bases on the assumption that a protein is nothing more than a tool engineered to perform a specific task. Thus, the protein,Äôs structure must encode its intended use and the inter-molecular communication system. Our study focuses on antifreeze proteins, which are particularly interesting since their function involves altering the properties of the solvent,Äîspecifically, preventing the formation of ice crystals.

Solvation Thermodynamics
Solvation Thermodynamics

Author: Arieh Y. Ben-Naim

Publisher: Springer Science & Business Media

Published: 2013-03-09

Total Pages: 253

ISBN-13: 1475765509

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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.