Protein Solvent Interactions

This work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.

A study of the thermodynamics of protein-protein and protein-ligand interactions. The author explains the energetics of protein interactions and gives a thorough account of the complicated biophysics that occur when the effects of multiple, complex molecules are taken into account.

This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.

In the areas of biochemistry and cell biology, characterizations of stability and molecular interactions call for a quantitative approach with a level of precision that matches the fine tuning of these interactions in a living cell. Supporting and up-dating previous Methods in Molecular BiologyTM volumes, Protein Structure, Stability, and Interactions approaches its subject with a focus on theory and practical applications for both established methods as well as exciting new procedures. The volume presents an overview of many techniques currently used to study protein stability and interactions, including scanning and titration calorimetry, spectroscopic methods, high field NMR, and analytical ultracentrifugation. As a volume of the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and easy to reference, Protein Structure, Stability, and Interactions is an ideal guide for all scientists interested in biomolecular interactions.

Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.

This book is aimed at understanding which molecular parameters control the thermodynamics, structure, and functions of the protein-water systems. Proteins are one of the most important classes of biological molecules. Water binding (hydration or biological water) plays a crucial role in determining the structure, stability, and functions of proteins. Knowledge of processes occurring upon hydration or dehydration of protein macromolecules is very important in biotechnological and pharmaceutical applications of proteins such as their use as biocatalysts, biosensors, and selective adsorbents. There are essential differences between hydration and bulk water surrounding a protein. This means that a characterisation of the hydration of protein macromolecules requires elucidating the effects of both the protein on water and vice versa. Therefore, a quantitative estimation of the protein and water contributions to the thermodynamic functions of binary protein-water systems is of considerable fundamental importance and practical interest. This book describes the basic principles of a novel methodology to investigate the protein-water interactions. This methodology is based on the analysis of the excess thermodynamic functions of mixing. The thermodynamic properties (volume V, enthalpy H, entropy S, heat capacity Cp, and Gibbs free energy G) of a real binary water-protein system can be expressed in terms of the excess functions. They are the difference between the thermodynamic function of mixing in a real system and the value corresponding to an ideal system at the same temperature, pressure and composition. For an ideal system, all excess functions are zero. Deviations of the excess functions from zero indicate the extent to which the studied binary system is non-ideal due to strong specific interactions between components (ie: hydrogen bonding and charge-charge interactions).

The book contains in its first part reviews on modelling of enzyme properties in organic solvents, lipase-catalysed synthesis of carboxylic amides, chemoenzymatic synthesis of lipidated peptides and chemoenzymatic transformations in nucleoside chemistry. In the second part contributions on recent developments in biocatalysis are given: lipase and esterase catalysed resolutions, investigations on regio- and stereoselective biocatalytic acylations in steroid side-chains and of substrate- and stereospecificity of Penicillin G amidases, deracemisation for amino acid synthesis, biocatalytic hydrolysis of nitriles, enzymatic and microbial hydroxylation of dienes and alpha-methyl esters, enantioselective sulphoxidations by peroxidases.

In additionto covering thoroughly the core areas of physical organic chemistry -structure and mechanism - this book will escortthe practitioner of organic chemistry into a field that has been thoroughlyupdated.