Download or read book Thermodynamic Investigation of Bio macromolecular Interactions written by Maryam Kabiri and published by . This book was released on 2014 with total page 176 pages. Available in PDF, EPUB and Kindle. Book excerpt: The spontaneous assembly of polypeptides through non-covalent interactions at physiological conditions is the main focus of the presented work and will be discussed from two different perspectives: (i) the interaction of peptide chains with themselves leading to formation of higher order structures (self-assembling peptides); (ii) the interaction of polypeptides with nano-sized surfaces (protein-nanoparticle interactions). Although self-assembling peptides are an important growing class of biomaterials, most of the works in this field have focused upon their various biomedical applications without highlighting the molecular mechanisms which result in their self-assembly into supra-molecular structures inside the body. Herein, through an in-depth thermodynamic analysis utilizing Isothermal Titration Calorimtry technique, the driving forces for self-assembly of ionic self-complementary peptide RADA4 and its variants were identified implying great contribution of molecular hydration and charge to the self-assembly process. Furthermore, the interfacial molecules involved in self-assembly of these molecules was experimentally quantified. It was found that appending five serine residues to C-terminus of RADA4 can overshadow the hydrophobic contribution of RADA segment leading to hydrogen bonding being the main driving force for self-assembly; while presence of 5 lysine residues inhibited RADA4 self-assembly. Secondly, the interaction of proteins with zwitterionic-modified nanoparticles (NPs) was investigated. Although widely studied, the underlying mechanism for the protein-repellent behavior of zwitterionic polymers is largely unknown. A set of thermodynamic investigations was performed to study the interaction of two model proteins (with distinctly different adsorption behaviour) with the surface of zwitterionic-modified silica nanoparticles. The nature of the interaction between proteins and polymer-modified nanoparticle was identified along with highlighting the main driving forces leading to their adsorption onto the nanoparticle's surface. Moreover, the impact of zwitterion's spacer length and end-group chemistry on thermodynamics of protein adsorption was analyzed. Overall, our results indicated that the main advantage of zwitterionic polymer modification of surfaces are: i) an increase in water molecules at the interface, ii) lack of counter-ion release from surfaces and iii) lower structural reorganization of the system upon protein-surface interaction. The findings presented in this work will fundamentally impact our understanding of nano-bio interfaces leading to development of more optimum nano-biomaterials in future.
Download or read book Linkage Thermodynamics of Macromolecular Interactions written by and published by Academic Press. This book was released on 1998-06-24 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume commemorates the 50th anniversary of the appearance in Volume 4 in 1948 of Dr. Jeffries Wyman's famous paper in which he "laid down" the foundations of linkage thermodynamics. Experts in this area contribute articles on the state-of-the-art of this important field and on new developments of the original theory. Among the topics covered in this volume are electrostatic contributions to molecular free energies in solution; site-specific analysis of mutational effects in proteins; allosteric transitions of the acetylcholine receptor; and deciphering the molecular code of hemoglobin allostery.
Download or read book Thermodynamics in Biology written by Enrico Di Cera and published by Oxford University Press, USA. This book was released on 2000 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enrico Di Cera, a rising star in biophysics, has organized a superb group of authors to write substantial chapters covering the most exciting and central issues relating to the bioenergetic aspects of proteins, nucleic acids, and their interactions. Topics covered in this book are protein and nucleic acid folding and stability, enzyme-substrate interactions, prediction of the affinity of complexes, electrostatics, and non-equilibrium aspects of protein function. The breadth of the topics covered in this book illustrates the growing importance of thermodynamic approaches in the study of biological phenomena. The book should be of wide interest to biophysicists, biochemists, and structural biologists.
Download or read book Energetics of Biological Macromolecules Part C written by and published by Elsevier. This book was released on 2000-08-09 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 323 of Methods in Enzymology is dedicated to the energetics of biological macromolecules. Understanding the molecular mechanisms underlying a biological process requires detailed knowledge of the structural relationships within the system and an equally detailed understanding of the energetic driving forces that control the structural interactions. This volume presents modern thermodynamic techniques currently being utilized to study the energetic driving forces in biological systems. It will be a useful reference source and textbook for scientists and students whose goal is to understand the energetic relationships between macromoleculer structures and biological functions. This volume supplements Volumes 259 and Volume 295 of Methods in Enzymology. Key Features * Probing Stability of Helical Transmembrane Proteins * Energetics of Vinca Alkaloid Interactions with Tubulin * Deriving Complex Ligand Binding Formulas * Mathematical Modeling of Cooperative Interactions in Hemoglobin * Analysis of Interactions of Regulatory Protein TyrR with DNA * Parsing Free Energy of Drug-DNA Interactions * Use of Fluorescence as Thermodynamics Tool
Download or read book Biothermodynamics Part B written by Michael L. Johnson and published by Academic Press. This book was released on 2009-11-11 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of thermodynamics in biological research can be equated to an energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well. This volume presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. Elucidates the relationships between structure and energetics and their applications to molecular design, aiding researchers in the design of medically important molecules Provides a "must-have" methods volume that keeps MIE buyers and online subscribers up-to-date with the latest research Offers step-by-step lab instructions, including necessary equipment, from a global research community
Download or read book Biomolecular Thermodynamics written by Douglas Barrick and published by CRC Press. This book was released on 2017-09-11 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: "an impressive text that addresses a glaring gap in the teaching of physical chemistry, being specifically focused on biologically-relevant systems along with a practical focus.... the ample problems and tutorials throughout are much appreciated." –Tobin R. Sosnick, Professor and Chair of Biochemistry and Molecular Biology, University of Chicago "Presents both the concepts and equations associated with statistical thermodynamics in a unique way that is at visual, intuitive, and rigorous. This approach will greatly benefit students at all levels." –Vijay S. Pande, Henry Dreyfus Professor of Chemistry, Stanford University "a masterful tour de force.... Barrick's rigor and scholarship come through in every chapter." –Rohit V. Pappu, Edwin H. Murty Professor of Engineering, Washington University in St. Louis This book provides a comprehensive, contemporary introduction to developing a quantitative understanding of how biological macromolecules behave using classical and statistical thermodynamics. The author focuses on practical skills needed to apply the underlying equations in real life examples. The text develops mechanistic models, showing how they connect to thermodynamic observables, presenting simulations of thermodynamic behavior, and analyzing experimental data. The reader is presented with plenty of exercises and problems to facilitate hands-on learning through mathematical simulation. Douglas E. Barrick is a professor in the Department of Biophysics at Johns Hopkins University. He earned his Ph.D. in biochemistry from Stanford University, and a Ph.D. in biophysics and structural biology from the University of Oregon.
Download or read book Equilibria and Kinetics of Biological Macromolecules written by Prof. Jan Hermans and published by John Wiley & Sons. This book was released on 2013-10-22 with total page 411 pages. Available in PDF, EPUB and Kindle. Book excerpt: Progressively builds a deep understanding of macromolecular behavior Based on each of the authors' roughly forty years of biophysics research and teaching experience, this text instills readers with a deep understanding of the biophysics of macromolecules. It sets a solid foundation in the basics by beginning with core physical concepts such as thermodynamics, quantum chemical models, molecular structure and interactions, and water and the hydrophobic effect. Next, the book examines statistical mechanics, protein-ligand binding, and conformational stability. Finally, the authors address kinetics and equilibria, exploring underlying theory, protein folding, and stochastic models. With its strong emphasis on molecular interactions, Equilibria and Kinetics of Biological Macromolecules offers new insights and perspectives on proteins and other macromolecules. The text features coverage of: Basic theory, applications, and new research findings Related topics in thermodynamics, quantum mechanics, statistical mechanics, and molecular simulations Principles and applications of molecular simulations in a dedicated chapter and interspersed throughout the text Macromolecular binding equilibria from the perspective of statistical mechanics Stochastic processes related to macromolecules Suggested readings at the end of each chapter include original research papers, reviews and monographs, enabling readers to explore individual topics in greater depth. At the end of the text, ten appendices offer refreshers on mathematical treatments, including probability, computational methods, Poisson equations, and defining molecular boundaries. With its classroom-tested pedagogical approach, Equilibria and Kinetics of Biological Macromolecules is recommended as a graduate-level textbook for biophysics courses and as a reference for researchers who want to strengthen their understanding of macromolecular behavior.
Download or read book Energetics of Biological Macromolecules written by Michael L. Johnson and published by Elsevier. This book was released on 1998 with total page 596 pages. Available in PDF, EPUB and Kindle. Book excerpt: Essential publication for researchers in all fields of life sciences. Key Features * Major topics covered include: * Deciphering rules of helix stability in peptides * Protein Folding in Membranes * Molecular Crowding * Study of the Bohr Effect in Hemoglobin Intermediates * Photoacoustic Calorimetry of Proteins * Theoretical Aspects of Isothermal Titration Calorimetry * Energetic Methods to Study Bifunctional Biotin Repressor.
Download or read book Thermodynamic Studies Concerning the Interaction of Water with Biological Macromolecules written by Stephen Lewis Zimmer and published by . This book was released on 1971 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biothermodynamics Part C written by and published by Academic Press. This book was released on 2010-12-28 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past several years, there has been an explosion in the ability of biologists, molecular biologists and biochemists to collect vast amounts of data on their systems. Biothermodynamics, Part C presents sophisticated methods for estimating the thermodynamic parameters of specific protein-protein, protein-DNA and small molecule interactions. The use of thermodynamics in biological research is used as an “energy book-keeping system. While the structure and function of a molecule is important, it is equally important to know what drives the energy force. These methods look to answer: What are the sources of energy that drive the function? Which of the pathways are of biological significance? As the base of macromolecular structures continues to expand through powerful techniques of molecular biology, such as X-ray crystal data and spectroscopy methods, the importance of tested and reliable methods for answering these questions will continue to expand as well. Elucidates the relationships between structure and energetics and their applications to molecular design, aiding researchers in the design of medically important molecules Provides a "must-have" methods volume that keeps MIE buyers and online subscribers up-to-date with the latest research Offers step-by-step lab instructions, including necessary equipment, from a global research community
Download or read book Thermodynamic Theory of Site Specific Binding Processes in Biological Macromolecules written by Enrico Di Cera and published by Cambridge University Press. This book was released on 1995-11-23 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Monograph on important subject in biochemistry and biophysics.
Download or read book Microcalorimetry of Macromolecules written by Peter L. Privalov and published by John Wiley & Sons. This book was released on 2012-07-31 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Examining the physical basis of the structure of macromolecules—proteins, nucleic acids, and their complexes—using calorimetric techniques Many scientists working in biology are unfamiliar with the basics of thermodynamics and its role in determining molecular structures. Yet measuring the heat of structural change a molecule undergoes under various conditions yields information on the energies involved and, thus, on the physical bases of the considered structures. Microcalorimetry of Macromolecules offers protein scientists unique access to this important information. Divided into thirteen chapters, the book introduces readers to the basics of thermodynamics as it applies to calorimetry, the evolution of the calorimetric technique, as well as how calorimetric techniques are used in the thermodynamic studies of macromolecules, detailing instruments for measuring the heat effects of various processes. Also provided is general information on the structure of biological macromolecules, proteins, and nucleic acids, focusing on the key thermodynamic problems relating to their structure. The book covers: The use of supersensitive calorimetric instruments, including micro and nano-calorimeters for measuring the heat of isothermal reactions (Isothermal Titration Nano-Calorimeter), the heat capacities over a broad temperature range (Scanning Nano-Calorimeter), and pressure effects (Pressure Perturbation Nano-Calorimeter) Two of the simplest but key structural elements: the α and polyproline helices and their complexes, the α-helical coiled-coil, and the pyroline coiled-coils Complicated macromolecular formations, including small globular proteins, multidomain proteins and their complexes, and nucleic acids Numerous examples of measuring the ground state of protein energetics, as well as changes seen when proteins interact The book also reveals how intertwined structure and thermodynamics are in terms of a macromolecule's organization, mechanism of formation, the stabilization of its three-dimensional structure, and ultimately, its function. The first book to describe microcalorimetric technique in detail, enough for graduate students and research scientists to successfully plumb the structural mysteries of proteins and the double helix, Microcalorimetry of Macromolecules is an essential introduction to using a microcalorimeter in biological studies.
Download or read book Kinetics for the Life Sciences written by H. Gutfreund and published by Cambridge University Press. This book was released on 1995-09-14 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of the book is to introduce the reader to the kinetic analysis of a wide range of biological processes at the molecular level. It is intended to show that the same approach can be used to resolve the number of steps in enzyme reactions, muscle contraction, visual perception and ligand binding receptors that trigger other physiological processes. Attention is also given to methods for characterizing these steps in chemical terms. Although the treatment is mainly theoretical, a wide range of examples and experimental techniques are also introduced and an historical approach is used to demonstrate the development of the theory and experimental techniques of kinetic analysis in biology.
Download or read book Energetics of Biological Macromolecules Part D written by Jo M. Holt and published by Elsevier. This book was released on 2004-04-02 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the cooperative binding aspects of energetics in biological macromolecules. Methodologies such as NMR, small-angle scattering techniques for analysis, calorimetric analysis, fluorescence quenching, and time resolved FRET measurements are discussed. *Methods for Evaluating Cooperativity in a Dimeric Hemoglobin*Multiple-Binding of Ligands to a Linear Biopolymer*Fluorescence Quenching Methods to Study Protein-Nucleic Acid Interactions*Linked Equilibria in Biotin Repressor Function: Thermodynamic, Structural and Kinetic Analysis
Download or read book Biophysics and Other Topics written by Aharon Katzir-Katchalsky and published by Academic Press. This book was released on 2013-10-22 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics and Other Topics: Selected Papers by Aharon Katzir-Katchalsky covers papers on polyelectrolytes, mechanochemistry, irreversible thermodynamics, membrane processes, network thermodynamics, biophysics, and science and humanities. The book discusses on polyelectrolytes, the electrostatic potential, thermodynamic properties, interaction with small molecules and ions, and cooperative transitions. The text also describes mechanochemistry; dynamics of macromolecular interactions; hysteresis; and memory. Irreversible thermodynamics, theory of membrane processes, and network thermodynamics are also considered. The book further tackles the reactions of amino acids with aldoses, polypeptide synthesis, and prebiotic synthesis. The text then encompasses topics on surface activity of polyelectrolytes; properties of the red cell membrane; and science and the humanities. People involved in the study of the above mentioned topics will find the book invaluable.
Download or read book Thermodynamic Signatures of Macromolecular Complexes Insights on the Stability and Interactions of Nucleoplasmin a Nuclear Chaperone written by Stefka G. Taneva and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Binding and Linkage written by Jeffries Wyman and published by University Science Books. This book was released on 1990 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ligand-macromolecule interactions are of fundamental importance in the control of biological processes. This book applies the principles of linkage thermodynamics to polyfunctional macromolecular systems under equilibrium conditions, and describes the binding, linkage, and feedback phenomena that lead to control of complex metabolic processes. The first chapter sets out the different processes (conformational changes, changes in state of aggregation, phase changes) involving biological macromolecules which are affected by chemical variables (such as ligands) or physical variables (such as temperature and pressure). The general effects of ligands on micromolecular conformations and interactions are illustrated with specific examples from the respiratory proteins, electron-transport proteins, and nucleic acid binding proteins. Subsequent chapters develop these themes, and describe in detail how the mathematics of regulation and control can be applied to macromolecules in biological system.
