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Author: Biman Bagchi
Publisher: Cambridge University Press
Published: 2013-11-14
Total Pages: 383
ISBN-13: 1107037298
DOWNLOAD EBOOKA unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.
Author: Masayoshi Nakasako
Publisher: Springer Nature
Published: 2021-10-25
Total Pages: 321
ISBN-13: 4431569197
DOWNLOAD EBOOKThis book describes hydration structures of proteins by combining experimental results with theoretical considerations. It is designed to introduce graduate students and researchers to microscopic views of the interactions between water and biological macromolecules and to provide them with an overview of the field. Topics on protein hydration from the past 25 years are examined, most of which involve crystallography, fluorescence measurements, and molecular dynamics simulations. In X-ray crystallography and molecular dynamics simulations, recent advances have accelerated the study of hydration structures over the entire surface of proteins. Experimentally, crystal structure analysis at cryogenic temperatures is advantageous in terms of visualizing the positions of hydration water molecules on the surfaces of proteins in their frozen-hydrated crystals. A set of massive data regarding hydration sites on protein surfaces provides an appropriate basis, enabling us to identify statistically significant trends in geometrical characteristics. Trajectories obtained from molecular dynamics simulations illustrate the motion of water molecules in the vicinity of protein surfaces at sufficiently high spatial and temporal resolution to study the influences of hydration on protein motion. Together with the results and implications of these studies, the physical principles of the measurement and simulation of protein hydration are briefly summarized at an undergraduate level. Further, the author presents recent results from statistical approaches to characterizing hydrogen-bond geometry in local hydration structures of proteins. The book equips readers to better understand the structures and modes of interaction at the interface between water and proteins. Referred to as “hydration structures”, they are the subject of much discussion, as they may help to answer the question of why water is indispensable for life at the molecular and atomic level.
Author: Bernard Pullman
Publisher: Springer
Published: 1981-08-31
Total Pages: 588
ISBN-13:
DOWNLOAD EBOOKProceedings of the 14th Jerusalem Symposium on Quantum Chemistry and Biochemistry, Jerusalem, Israel, April 13-16, 1981
Author: Isabel Moraes
Publisher: Springer
Published: 2016-08-23
Total Pages: 188
ISBN-13: 3319350722
DOWNLOAD EBOOKThis book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.
Author: Vladimir A. Sirotkin
Publisher:
Published: 2019
Total Pages: 0
ISBN-13: 9781536160208
DOWNLOAD EBOOKThis book describes the basic principles of a novel methodology to investigate the preferential hydration and solvation of proteins in ternary protein-water-organic solvent systems. Protein-water interactions are well-known to play a critical role in determining the function, structure, and stability of protein macromolecules. Elucidation of the processes occurring upon protein hydration in the presence of third component (organic solvents, salts, urea) is essential in a wide range of biophysical, biomedical, and biotechnological applications. In particular, there are many advantages in employing water-poor organic solvents, including the suppression of undesirable side reactions caused by water, the biocatalysis of reversed hydrolytic reactions (transesterification, peptide synthesis), or increased thermostability. Distinct intermediate protein states induced by organic solvents may be responsible for numerous neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, and Huntington's disease). However, the manner in which organic solvents increase/decrease the thermal stability, induce/reduce the extent of denaturation, and stabilize/destabilize the partially folded conformations of proteins (amyloid fibrils and molten globules) is an intricate function of water content in organic liquids. Preferential hydration/solvation is an effective method for revealing the mechanism of the protein stabilization or denaturation. When a protein interacts with a binary water-organic solvent mixture, the three components do not equally mix. Water or organic solvent molecules exist preferentially in the protein's solvation shell. This difference between the solvation shell and bulk solvent in the solvent components has been termed preferential solvation. Preferential solvation is a thermodynamic quantity that describes the protein surface occupancy by the water and cosolvent molecules. This is associated with the actual numbers of water/cosolvent molecules that are in contact with the protein's surface. It was also found that the protein destabilization is directly associated with the preferential binding of the denaturant molecules to specific protein groups.The aim of our study is to monitor the preferential solvation and preferential hydration of the protein macromolecules at low, intermediate, and high water content in organic solvents at 25 oC. Our approach is based on the simultaneous measurements of the absolute values of the water and organic solvent sorption. The preferential solvation/hydration parameters were calculated using the water and organic solvent sorption values. The preferential solvation/hydration parameters were compared with the corresponding changes in the protein structure that transpire regarding the interaction of the protein with organic solvent and water molecules. The effect of organic solvent on the protein structure was investigated by FTIR (Fourier Transform Infrared) spectroscopy.
Author: Gertz I. Likhtenshtein
Publisher: Springer Nature
Published: 2021-10-21
Total Pages: 523
ISBN-13: 3030825035
DOWNLOAD EBOOKThis book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.
Author: Westhof
Publisher: CRC Press
Published: 1993-08-16
Total Pages: 492
ISBN-13: 9780849375705
DOWNLOAD EBOOKWater and Biological Macromolecules presents an excellent description of the structural aspects of water molecules around biological macromolecules. Topics discussed include the properties of water in solid and liquid states; proteins, nucleic acids, polysaccharides, and lipids; and theoretical approaches for understanding the macroscopic observations and integrating microscopic descriptions. The nature and roles of hydration forces in macromolecular complexation and cell-cell interactions are explained, in addition to phenomena such as entropy-enthalpy compensation and the thermodynamic treatment of water bridging. Water and Biological Macromolecules will be a valuable reference for biophysicists, biochemists, and macromolecular biologists.
Author: Vladimir A. Sirotkin
Publisher: Nova Science Publishers
Published: 2014
Total Pages: 0
ISBN-13: 9781634630078
DOWNLOAD EBOOKThis 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).
Author: Roger Gregory
Publisher: CRC Press
Published: 2024-11-01
Total Pages: 596
ISBN-13: 1040282512
DOWNLOAD EBOOKThis 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.
Author: E. Anibal Disalvo
Publisher: Springer
Published: 2015-10-05
Total Pages: 295
ISBN-13: 3319190601
DOWNLOAD EBOOKThis book is about the importance of water in determining the structure, stability and responsive behavior of biological membranes. Water confers to lipid membranes unique features in terms of surface and mechanical properties. The analysis of the hydration forces, plasticiser effects, controlled hydration, formation of microdomains of confined water suggests that water is an active constituent in a water-lipid system. The chapters describe water organization at the lipid membrane–water interphase, the water penetration, the long range water structure in the presence of lipid membranes by means of X-ray and neutron scattering, general polarization, fluorescent probes, ATR-FTIR and near infrared spectroscopies, piezo electric methods, computer simulation and surface thermodynamics. Permeation, percolation, osmotic stress, polarization, protrusion, sorption, hydrophobicity, density fluctuations are treated in detail in self-assembled bilayers. Studies in lipid monolayers show the correlation of surface pressure with water activity and its role in peptide and enzyme interactions. The book concludes with a discussion on anhydrobiosis and the effect of water replacement in microdomains and its consequence for cell function. New definitions of lipid/water interphases consider water not only as a structural-making solvent but as a mediator in signalling metabolic activity, modulating protein insertion and enzymatic activity, triggering oscillatory reactions and functioning of membrane bound receptors. Since these effects occur at the molecular level, membrane hydration appears fundamental to understand the behavior of nano systems and confined environments mimicking biological systems. These insights in structural, thermodynamical and mechanical water properties give a base for new paradigms in membrane structure and function for those interested in biophysics, physical chemistry, biology, bio and nano medicine, biochemistry, biotechnology and nano sciences searching for biotechnological inputs in human health, food industry, plant growing and energy conversion.
