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Author : Jeszenői Norbert
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (18 download)
Download or read book Calculation of Hydration Structures of Proteins and Their Complexes written by Jeszenői Norbert and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Masayoshi Nakasako
Publisher :
ISBN 13 : 9784431569183
Total Pages : 0 pages
Book Rating : 4.5/5 (691 download)
Download or read book Hydration Structures of Proteins written by Masayoshi Nakasako and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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 : Biman Bagchi
Publisher : Cambridge University Press
ISBN 13 : 1107037298
Total Pages : 383 pages
Book Rating : 4.1/5 (7 download)
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.
Author : Dev Bukhsh Singh
Publisher : Springer Nature
ISBN 13 : 9811555303
Total Pages : 458 pages
Book Rating : 4.8/5 (115 download)
Download or read book Frontiers in Protein Structure, Function, and Dynamics written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-07-02 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.
Author : Masayoshi Nakasako
Publisher : Springer Nature
ISBN 13 : 4431569197
Total Pages : 321 pages
Book Rating : 4.4/5 (315 download)
Download or read book Hydration Structures of Proteins written by Masayoshi Nakasako and published by Springer Nature. This book was released on 2021-10-25 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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 : Westhof
Publisher : CRC Press
ISBN 13 :
Total Pages : 488 pages
Book Rating : 4.3/5 (91 download)
Download or read book Water and Biological Macromolecules written by Westhof and published by CRC Press. This book was released on 1993-08-16 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Water structure. Termadynamic and dynamic properties of water. Hydratyon of amino acids in protein crystals. Water structure of crystallized proteins: high-resolution studies. Hydration of proteins secondary structures-the role in protein folding. Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. Structural water bridges in nucleic acids. Hydration sites and hydration bridges around DNA helices. Light scattering spectroscopy studies of the water molecules in DNA. Polysacaride interactions with water. The role of structural water molecules in protein-sccharide complexes. Lipid hydration. Hydration forces. Solvation thermodynamics of biopolymers.
Author : Marie-Claire Bellissent-Funel
Publisher : IOS Press
ISBN 13 : 9789051994391
Total Pages : 456 pages
Book Rating : 4.9/5 (943 download)
Download or read book Hydration Processes in Biology written by Marie-Claire Bellissent-Funel and published by IOS Press. This book was released on 1999 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: The interaction of water at organic surfaces or interfaces is of fundamental and technological interest and importance in chemistry, physics and biology. Progress towards an in-depth, molecular interpretation of the structure and dynamics of interfacial water needs a range of novel experimental and simulation techniques. We are now reaching the stage at which we understand, at the molecular level, the mutual perturbation at a macromolecule/water interface. The aims of this book are to provide with a comprehensive background to the properties of bulk water at the microscopic level and with a substantial account of the theoretical and experimental contributions which have been done to understand the role of water in various systems from some model systems to the more complex ones such as the biological systems.
Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.3/5 (321 download)
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : N. Rama Krishna
Publisher : Springer Science & Business Media
ISBN 13 : 0306470845
Total Pages : 565 pages
Book Rating : 4.3/5 (64 download)
Download or read book Structure Computation and Dynamics in Protein NMR written by N. Rama Krishna and published by Springer Science & Business Media. This book was released on 2006-05-09 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 17 is the second in a special topic series devoted to modern techniques in protein NMR, under the Biological Magnetic Resonance series. Volume 16, with the subtitle Modern Techniques in Protein NMR , is the first in this series. These two volumes present some of the recent, significant advances in the biomolecular NMR field with emphasis on developments during the last five years. We are honored to have brought together in these volume some of the world s foremost experts who have provided broad leadership in advancing this field. Volume 16 contains - vances in two broad categories: I. Large Proteins, Complexes, and Membrane Proteins and II. Pulse Methods. Volume 17 contains major advances in: I. Com- tational Methods and II. Structure and Dynamics. The opening chapter of volume 17 starts with a consideration of some important aspects of modeling from spectroscopic and diffraction data by Wilfred van Gunsteren and his colleagues. The next two chapters deal with combined automated assignments and protein structure determination, an area of intense research in many laboratories since the traditional manual methods are often inadequate or laborious in handling large volumes of NMR data on large proteins. First, Werner Braun and his associates describe their experience with the NOAH/DIAMOD protocol developed in their laboratory.
Author : Nobuo Niimura
Publisher : Oxford University Press
ISBN 13 : 0191004812
Total Pages : 250 pages
Book Rating : 4.1/5 (91 download)
Download or read book Neutron Protein Crystallography written by Nobuo Niimura and published by Oxford University Press. This book was released on 2011-02-17 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is one of the first books dedicated to the emerging field of neutron protein crystallography (NPC). The text covers all of the practical aspects of NPC, from the basic background of neutron scattering and diffraction, to the technical details of neutron facilities, growth of high-quality crystals, and data analysis. The final chapter is devoted to providing many examples of using NPC to investigate a wide range of different proteins. It demonstrates how NPC can explore hydrogen bonds, protonation and deprotonation of amino acid residues, hydration structures, and hydrogen-to-deuterium exchange ratios. To avoid redundancy with other textbooks on X-ray protein crystallography (XPC), this book assumes a familiarity with the basics of XPC and strives to highlight and explain the differences between XPC and NPC. It is therefore especially useful for X-ray protein crystallographers who are eager to have a sound, scientific basis for judging if NPC is the right technique for furthering their experimental programs.
Author : Vladimir N. Uversky
Publisher : Nova Publishers
ISBN 13 : 9781600217043
Total Pages : 414 pages
Book Rating : 4.2/5 (17 download)
Download or read book Methods in Protein Structure and Stability Analysis: Conformational stability, size, shape, and surface of protein molecules written by Vladimir N. Uversky and published by Nova Publishers. This book was released on 2007 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein research is a frontier field in science. Proteins are widely distributed in plants and animals and are the principal constituents of the protoplasm of all cells, and consist essentially of combinations of a-amino acids in peptide linkages. Twenty different amino acids are commonly found in proteins, and serve as enzymes, structural elements, hormones, immunoglobulins, etc., and are involved throughout the body, and in photosynthesis. This book gathers new leading-edge research from throughout the world in this exciting and exploding field of research.
Author : Jack Kyte
Publisher : Garland Science
ISBN 13 : 1136843515
Total Pages : 832 pages
Book Rating : 4.1/5 (368 download)
Download or read book Structure in Protein Chemistry written by Jack Kyte and published by Garland Science. This book was released on 2006-11-01 with total page 832 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of Structure in Protein Chemistry showcases the latest developments and innovations in the field of protein structure analysis and prediction. The book begins by explaining how proteins are purified and describes methods for elucidating their sequences of amino acids and defining their posttranslational modifications. Comprehensive explanations of crystallography and of noncovalent forces-ionic interactions, hydrogen bonding, and the hydrophobic effect-act as a prelude to an exhaustive description of the atomic details of the structures of proteins. The resulting understanding of protein molecular structure forms the basis for discussions of the evolution of proteins, the symmetry of the oligomeric associations that produce them, and the chemical, mathematical, and physical basis of the techniques used to study their structures. The latter include image reconstruction, nuclear magnetic resonance spectroscopy, proton exchange, optical spectroscopy, electrophoresis, covalent cross-linking, chemical modification, immunochemistry, hydrodynamics, and the scattering of light, X-radiation, and neutrons. These procedures are applied to study the folding of polypeptides and the assembly of oligomers. Biological membranes and their proteins are also discussed. Structure in Protein Chemistry, Second Edition, bridges the gap between introductory biophysical chemistry courses and research literature. It serves as a comprehensive textbook for advanced undergraduates and graduate students in biochemistry, biophysics, and structural and molecular biology. Professionals engaged in chemical, biochemical, and molecular biological research will find it a useful reference.
Author : Christo Christov
Publisher : Academic Press
ISBN 13 : 0123864852
Total Pages : 360 pages
Book Rating : 4.1/5 (238 download)
Download or read book Computational Chemistry Methods in Structural Biology written by Christo Christov and published by Academic Press. This book was released on 2011-09-23 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology serial has been a continuous, essential resource for protein chemists. Covering reviews of methodology and research in all aspects of protein chemistry, including purification/expression, proteomics, modeling and structural determination and design, each volume brings forth new information about protocols and analysis of proteins while presenting the most recent findings from leading experts in a broad range of protein-related topics. This volume features articles on Computational Chemistry methods in Structural Biology. Essential resource for protein chemists This volume features articles on Computational Chemistry methods in Structural Biology
Author : John G. Kirkwood
Publisher : CRC Press
ISBN 13 : 9780677010304
Total Pages : 320 pages
Book Rating : 4.0/5 (13 download)
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:
Author : Martin Zacharias
Publisher : World Scientific
ISBN 13 : 1848163401
Total Pages : 401 pages
Book Rating : 4.8/5 (481 download)
Download or read book Protein-protein Complexes written by Martin Zacharias and published by World Scientific. This book was released on 2010 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etcetera.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.
Author : Jouko J. Virtanen
Publisher :
ISBN 13 : 9781267247902
Total Pages : 185 pages
Book Rating : 4.2/5 (479 download)
Download or read book Modeling the Hydration Layer Around Proteins and Nucleic Acids written by Jouko J. Virtanen and published by . This book was released on 2012 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: We develop a theory, termed HyPred, for describing the hydration shells of biological macromolecules and use the model to calculate accurate small/wide angle X-ray scattering (SWAXS), study protein-RNA binding, and calculate electrostatic energies of hydration. HyPred is developed using the approximation that a solute molecule's hydration is determined by local interactions and that long range interactions may be neglected. Thus, by examining the hydration of several different biological macromolecules, the hydration of other similar molecules (e.g., proteins, RNA, DNA) can be predicted since each class has similar surface chemical properties. More specifically all-atom explicit solvent molecular dynamics simulations are performed for several proteins and nucleic acids, and proximal radial distribution functions (pRDFs) are calculated by finding the average solvent density in each cube of a discretized representation of the simulation boxes and then evaluating the average density of cubes as a function of distance from the nearest solute atom and a function of the atom type of the nearest solute atom. This model is validated by reproducing the solvent densities found in the MD simulations and comparing the locations of predicted crystallographic water molecules to experiment. The HyPred model is then further validated by comparing calculated SWAXS patterns of proteins, hydrated by HyPred, to experimental data. The HyPred model is improved by the addition of the dependence of the pRDFs on the second nearest neighbor, the angle formed by the cube, the atom, and the atom to which the nearest solute atom is bonded to, and the local geometry of the solute. HyPred is then extended to model the hydration layer of nucleic acids enabling the study of protein-RNA complexes using HyPred. Finally, HyPred is extended to predict the charge density and the electrostatic energies of hydration and electrostatic potential energy maps.
Author : Vladimir A. Sirotkin
Publisher :
ISBN 13 : 9781536160208
Total Pages : 0 pages
Book Rating : 4.1/5 (62 download)
Download or read book Preferential Solvation and Hydration of Proteins in Water-organic Mixtures: written by Vladimir A. Sirotkin and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
