Water And Biological Macromolecules

Author by : Anonim
Languange : en
Publisher by : Macmillan International Higher Education
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Dynamics Of Biological Macromolecules By Neutron Scattering

Author by : Salvatore Magazù
Languange : en
Publisher by : Bentham Science Publishers
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Description : Dynamics of Biological Macromolecules by Neutron Scattering provides insight into the study of the dynamics of biological macromolecules by neutron scattering techniques. The applicability of neutron scattering to expanding fields of biological studies is


The Role Of Water In Determining Structure And Function Of Macromolecules And Macromolecular Assemblies

Author by : Nola L. Fuller
Languange : en
Publisher by : Unknown
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Description : The interaction of biological molecules with water is an important determinant of structural properties both in molecular assemblies, and in conformation of individual macromolecules. By observing the effects of manipulating the activity of water (which can be accomplished by limiting its concentration or by adding additional solutes, "osmotic stress"), one can learn something about intrinsic physical properties of biological molecules as well as measure an energetic contribution of closely associated water molecules to overall equilibria in biological reactions. Here two such studies are reported. The first of these examines several species of lysolipid which, while present in relatively low concentrations in biomembranes, have been shown to affect many cellular processes involving membrane-protein or membrane-membrane interactions. Monolayer elastic constants were determined by combining X-ray diffraction and the osmotic stress technique. Spontaneous radii of curvature of lysophosphatidylcholines were determined to be positive and in the range +30A to +70A, while lysophosphatidylethanolamines proved to be essentially flat. Neither lysolipid significantly affected the bending modulus of the monolayer in which it was incorporated. The second study examines the role of water in theprocess of polymerization of actin into filaments. Water activity was manipulated by adding osmolytes and the effect on the equilibrium dissociation constant (measured as the criticalmonomer concentration) was determined. As water activity was decreased, the critical concentration was reduced for Ca-actin but not for Mg-actin, suggesting that 10-12 fewer water molecules are associated with Ca-actin in the polymerized state. Thisunexpectedly small amount of water is discussed in the context of the common structural motif of a nucleotide binding cleft.


Hydration Of Biological Macromolecules

Author by : Anonim
Languange : en
Publisher by : Unknown
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Description : A method that uses two- and three-particle correlation functions between solute atoms and water molecules to approximate the density profile of water surrounding biomolecules. The method is based on a potential of mean force expansion and uses X-ray crystallography, NMR, or modeling structural input information on the biomolecule. For small, hydrophobic solutes, we have calculated entropies of hydration using the predicted water densities that are in good agreement with experimental results., We have also predicted the hydration of the catabolite activator protein-DNA complex. The method is extremely efficient and makes possible the study if hydration of large molecules with CPU minutes.


Hydration Structures Of Proteins

Author by : Masayoshi Nakasako
Languange : en
Publisher by : Springer Nature
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Description : 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.


From Molecules To Medicines

Author by : Joel L. Sussman
Languange : en
Publisher by : Springer Science & Business Media
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Description : Proceedings of the NATO Advanced Study Institute on Integrating Crystallography in the Fight Against Terrorism Erice, Italy 29 May-8 June 2008


Molecular Dynamics

Author by : Lichang Wang
Languange : en
Publisher by : BoD – Books on Demand
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Description : Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines


Spectroscopy Of Biological Molecules

Author by : M.P. Marques
Languange : en
Publisher by : IOS Press
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Description : This book presents contributions from some of the leading experts in spectroscopic techniques including infrared, Raman, NMR, fluorescence and Circular Dichroism spectroscopy. Structural characterization of biomolecules, cells, tissues and whole organisms are amongst the topics that were covered by these experts at the 14th European Conference on Spectroscopy of Biological Molecules (ECSBM2011), held at the University of Coimbra, Portugal, from 29th August to 3rd September 2011, of which this book contains the papers. The book would be particularly valuable for those interested in vibrational spectroscopy and imaging of cells and tissues, applications of spectroscopy in biotechnology, single cell studies and microbial characterization. It highlights the potential of spectroscopy and imaging in medical diagnosis and screening, and discusses issues related to methodology, including data acquisition, analysis and processing, that would be valuable for scientists who are new to the field. The book would be an important reference source for scientists in academia and industry as well as early stage researchers such as graduate students and post-doctoral researchers.


Aqueous Artefacts The Riddle Of Bound Water

Author by : John B. Bateman
Languange : en
Publisher by : Unknown
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Description : This paper, intended for the general reader, first discusses early ideas about water binding in biological systems. More recent work is presented in the form of a report and commentary on lectures given during a Royal Society discussion meeting, together with occasional references to other literature and to papers given at a somewhat similar symposium in Roscoff. The conclusion to be drawn is probably that although the acceptable definition of bound water is in doubt and the interpretation of experimental data frequently ambiguous, water binding to biological macromolecules to the extent of about 0.3 - 0.5 g.water/g.dry weight is fairly general. Further, there is evidence that the rates of many biological reactions may be controlled both by direct consumptive participation and by catalytic shifts of water molecules attached in and around receptor sites. A current controversy concerning the role of 'structured' water in active transport recalls similar disputes among the earlier proponents and opponents of water binding, dating probably from Overton's introduction of the idea in 1902.


Introduction To The Biophysics Of Activated Water

Author by : Igor Smirnov
Languange : en
Publisher by : Universal-Publishers
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Description : This is the first book to reveal the mechanism of 'long-term water memory' effects. The theory is based on precise mathematical calculations and a fundamental physical model of clathrate hydrates developed by Pauling in 1959. This book gives a detailed review of modern theories dealing with structure and properties of water. It also provides theory regarding the effect of activated water on biological systems under the life suppressive conditions such as ionizing and non-ionizing radiation. In addition, it provides detail information regarding the mechanism of DNA self-reparation process under the influence of activated water. Also included is a chapter on the innovative patented technology based on mechanism of 'long-term water memory' to prove the feasilibity with experimental data and protocols.


Spectroscopy Of Biological Molecules New Directions

Author by : Jan Greve
Languange : en
Publisher by : Springer Science & Business Media
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Description : Investigation of the structure and function of biological molecules through spectroscopic methods is a field rich in revealing, clever techniques and demanding experiments. It is most gratifying to see that the basic concepts are applied to more and more complex systems, making feasible the study of the behaviour of whole systems in relation to molecular disturbances. The analytical potential of spectroscopy and spectroscopic imaging enables species identification of bacteria and tissue recognition. Clear opportunities for in vivo applications become apparent in the medical field. The methods developed in biophysics start to generate spin-off in the direction of biotechnology, where in previous years we have seen this happen for biochemical techniques. New directions are manifest. Tools are being developed to investigate the behaviour of single molecules in interaction with their environment. Individual interactions can now be investigated and individual molecules in complexes can be visualized. Processes that were previously unobservable as a result of ensemble averaging can now be investigated on a single molecule level. Completely new information with regard to molecular behaviour is obtained in this way. The insights amaze us and the prospect that this development will continue is exciting. The 8th European Conference on the Spectroscopy of Biological Molecules is proud to have contributed to the dissemination of these new directions. This proceedings book is an appropriate reflection of the progress obtained so far in the spectroscopy of biological molecules.


Energetics Of Biological Macromolecules

Author by : Jo M. Holt
Languange : en
Publisher by : Elsevier
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Description : 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


Spectroscopy Of Biological Molecules

Author by : Jean Claude Merlin
Languange : en
Publisher by : Springer Science & Business Media
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Description : 6th European Conference on the Spectroscopy of Biological Molecules, 3--8 September 1995, Villeneuve d'Ascq, France


Nuclear Magnetic Resonance Of Biological Macromolecules

Author by : Anonim
Languange : en
Publisher by : Academic Press
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Description : The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences. Nuclear Magnetic Resonance of Biological Macromolecules, Part C is written with a "hands-on" perspective. That is, practical applications with critical evaluations of methodologies and experimental considerations needed to design, execute, and interpret NMR experiments pertinent to biological molecules. * One of the most highly respected publications in the field of biochemistry since 1955 * Frequently consulted, and praised by researchers and reviewers alike * Truly an essential publication for anyone in any field of the life sciences


Protein Water Interactions

Author by : Vladimir A. Sirotkin
Languange : en
Publisher by : Nova Science Pub Incorporated
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Description : 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).


Dielectric Relaxation In Biological Systems

Author by : Valerica Raicu
Languange : en
Publisher by : OUP Oxford
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Description : The study of dielectric properties of biological systems and their components is important not only for fundamental scientific knowledge but also for its applications in medicine, biology, and biotechnology. The associated technique - known as dielectric spectroscopy - has enabled researchers to quickly and accurately acquire time- or frequency-spectra of permittivity and conductivity and permitted the derivation and testing of realistic electrical models for cells and organelles. This text covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems. The authors' combined efforts provide a comprehensive and cohesive book that takes advantage of the expertise of multiple scientists involved in cutting-edge research in the specific sub-fields of bio-dielectric spectroscopy while maintaining its self-consistency through numerous discussions. The first six chapters cover theoretical, methodological and experimental aspects of relaxation and dispersion in biological dielectrics at molecular, cellular and cellular aggregate level. Applications are presented in the following chapters which are organized in the order of increased complexity, beginning with pure water, amino acids and proteins, continuing with vesicles and simple cells such as erythrocytes, and then with more complex, organelle-containing cells and cellular aggregates. Due to its broad coverage, the text could be used as a reference book by researchers, and as a textbook for upper-level undergraduate classes and graduate classes in (bio) physics, medical physics, quantitative biology, and engineering.


Dielectric Behaviour Of Water In Biological Material With Particular Reference To Brain Tissue

Author by : E. H. Grant
Languange : en
Publisher by : Unknown
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Description : The absorption of microwave energy by biological material at frequencies in excess of 1 GHz is due mainly to the water content. Knowledge of the dielectric properties of water in biological material is therefore a necessary prerequisite for the calculation of energy deposition. However, the water of hydration immediately adjacent to biological macromolecules is subject to chemical forces different from those in bulk water and must in consequence exhibit different dielectric properties. The nature and proportion of this water vary considerably fro one tissue to another and therefore need to be evaluated for each specific case. For adult-rabbit brain material, dielectric measurements show that the water of hydration constitutes about 20% of the total while the remainder has dielectric properties similar to those of pure water. With brain tissue from recently born rabbits, the proportion of water of hydration is indistinguishable from zero.


Equilibria And Kinetics Of Biological Macromolecules

Author by : Prof. Jan Hermans
Languange : en
Publisher by : John Wiley & Sons
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Description : 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.


Bios Instant Notes In Chemistry For Biologists

Author by : J Fisher
Languange : en
Publisher by : Taylor & Francis
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Description : BIOS Instant Notes Chemistry for Biologists, Third Edition, is the perfect text for undergraduates looking for a concise introduction to the subject, or a study guide to use before examinations. Each topic begins with a summary of essential facts-an ideal revision checklist-followed by a description of the subject that focuses on core information, with clear, simple diagrams that are easy for students to understand and recall in essays and exams. BIOS Instant Notes Chemistry for Biologists, Third Edition, is fully up-to-date and covers: The elements Chemical bonds and molecular shape Water- the biological solvent Carbon, the basis for life on Earth 3D-molecular structure of organic compounds Small inorganic molecules of biological importance Some metals in biology Molecular interactions Common reaction types of carbon based compounds Organic compounds by chemical class Aromatic compunds Chemical synthesis of biological molecules Important biological macromolecules by class Aqueous behaviour Elementary thermodynamics Kinetics Spectroscopy Units and calculations


Tour Of The Cell Water Carbohydrates And Lipids

Author by : The Open The Open Courses Library
Languange : en
Publisher by : Unknown
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Description : Tour of the Cell: Water, Carbohydrates and Lipids Loeb is referring to the Nobel Prize-winning experiments of Eduard Buchner, who proved that cells are not necessary for cellular chemical reactions to take place. This was one of the crucial steps toward the synthesis of biology and chemistry that culminates in the modern-day discipline we call biochemistry. The properties of matter are important in the study of biochemistry (and biology), so we need to introduce some chemical concepts to help us with that understanding. At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. Chapter Outline: Atoms, Isotopes, Ions, and Molecules: The Building Blocks Water: the Molecule of Life Introduction to Biological Molecules Chemical Reactions of Biological Macromolecules Carbohydrates Lipids Components and Structure of Plasmal Membranes The Open Courses Library introduces you to the best Open Source Courses.


Studies Of Structure Hydration And Dynamics Of Biological Macromolecules By Use Of Nmr Spectroscopy

Author by : Anonim
Languange : en
Publisher by : Unknown
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Description : Nuclear magnetic resonance (NMR) has emerged as a powerful tool for studying biological macromolecules in aqueous solution. This dissertation describes the efforts to study the structure, hydration and dynamics of biological macromolecules by solution state NMR spectroscopy. There are three projects covered by the dissertation: (i) polypeptide hydration studied by NMR in supercooled water; (ii) structure determination of protein AQ-1857 by NMR spectroscopy and (iii) base flipping mechanism of M. Hha I DNA methyltransferase. Chapter 1 gives brief introduction of NMR applications in biological sciences. Chapter 2 describes the first investigation of polypeptide hydration in supercooled water at temperatures down to -18, which allowed identification of the zero crossing points of intermolecular NOEs between hydration water protons and peptide protons. The experimental results were then fitted to spatial motional models to calculate the translational diffusion coefficients of different hydration water molecules. Chapter 3 presents data collection, spectral analysis and structure calculation of the NESGC target protein AQ-1857, pursued in the context of high-throughput structure determination efforts for structural genomics. Chapter 4, the centerpiece of this dissertation, describes the tremendous efforts in investigating the base flipping mechanism of M. Hha I DNA methyltransferase, including enzymatic synthesis of a partially 13 C, 15 N labeled cognate DNA duplex and the NMR studies on the MTase-DNA complexes. The ample NMR information from chemical shifts, line widths and peak intensities, and imino proton exchange rates provided new insights for understanding the base flipping process.


Bound Water In Biological Integrity

Author by : S. J. Webb
Languange : en
Publisher by : Springfield, Ill. : C.C. Thomas
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Energetics Of Biological Macromolecules

Author by : Michael L. Johnson
Languange : en
Publisher by : Elsevier
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Total Read : 22
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Description : General Description of the Volume: The very existence of biological structures and their functional interactions are dictated by energetic relationships. Thus the central theme of this volume is that thermodynamic methods, i.e. techniques that probe the energetics of biological macromolecules, now comprise a powerful and practical family of tools for research in modern biology. The application of thermodynamics and statistical thermodynamics to biochemical and biophysical systems is presented. This volume supplements Methods in Enzymology, Volume 259. General Description of the Series: The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an 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


Water In Biological Systems

Author by : Maksim Filippovich Vuks
Languange : en
Publisher by : Unknown
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Siavbhau Ju Nuay Garukosaly 1987 1988

Author by : Anonim
Languange : en
Publisher by : Unknown
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Description : Pedagogy and guidance for primary teachers.


Intermolecular Structure And Dynamics Of Aqueous N Methylacetamide

Author by : Susan Kathryn Allison
Languange : en
Publisher by : Unknown
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Description : The twin questions of how and why protein molecules fold into the specific topologies which enable them to fulfill their biological function have been the subject of continuous scientific investigation since the early twentieth century. Interactions between biological macromolecules and water are obviously crucial to both folding and function but attempts to gain understanding are impeded by the size and complexity of these systems. A useful approach is to consider much simpler model systems which capture some essential element of real biological systems but are experimentally and theoretically tractable. N-methylacetamide (NMA) is a minimal model of the peptide linkage which forms the backbone of protein molecules. Its behaviour in aqueous solution therefore captures the important competition between peptide - peptide and peptide - water hydrogen bonds which arises in protein hydration. In this thesis aqueous NMA solutions are studied across the full concentration range using classical molecular dynamics simulation. This gives access to the complete spectrum of behaviour between the two important limiting cases of dilute NMA in water and, conversely, dilute water in NMA. Water is now known to be an active player in biological interactions and the simple system studied here displays significant disruption of the structure and dynamics of pure water with the addition of only a small proportion of peptide groups. At dilute NMA concentrations water molecules continue to form system-size hydrogen bonded networks. Water molecules appear to optimise their local tetrahedral order by forming hydrogen bonds with a combination of NMA and water neighbours, rather than solely with members of their own species. NMA molecules hydrogen bond through the amide and carbonyl groups to form linear and branched chains in both the pure liquid and in the aqueous solutions. In the NMA rich region water molecules preferentially donate both hydrogens to chain-end or midchain carbonyl oxygens, forming bridges between NMA chains which resemble buried water configurations found in protein cavities. These bridge structures are thought to contribute to the observed slowing of the system dynamics at these concentrations. The investigation of dynamics by classical simulation is complemented by a quasielastic neutron scattering study of NMA in its liquid and aqueous phases.


Energetics Of Biological Macromolecules

Author by : Anonim
Languange : en
Publisher by : Elsevier
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Description : 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