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Molecular Simulations And Biomembranes

Author: Mark S. P. Sansom
Publisher: Royal Society of Chemistry
ISBN: 0854041893
Size: 79.56 MB
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The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.

Biomembrane Frontiers

Author: Thomas Jue
Publisher: Springer Science & Business Media
ISBN: 160761314X
Size: 56.61 MB
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This is the second book in the Handbook of Modern Biophysics series, dedicated to fundamental topics and new applications in biophysics. This book on biomembranes covers theory and application and includes problem sets, references and guides for further study.

Biomembrane Simulations

Author: Max L. Berkowitz
Publisher: CRC Press
ISBN: 1351060295
Size: 35.55 MB
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Due to recent advancements in the development of numerical algorithms and computational hardware, computer simulations of biological membranes, often requiring use of substantial computational resources, are now reaching a mature stage. Since molecular processes in membranes occur on a multitude of spatial and time scales, molecular simulations of membranes can also serve as a testing ground for use of multi-scale simulation techniques. This book addresses some of the important issues related to understanding properties and behavior of model biological membranes and it Shows how simulations improve our understanding of biological membranes and makes connections with experimental results. Presents a careful discussion of the force fields used in the membrane simulations including detailed all-atom fields and coarse-grained fields. Presents a continuum description of membranes. Discusses a variety of issues such as influence of membrane surfaces on properties of water, interaction between membranes across water, nanoparticle permeation across the membrane, action of anesthetics and creation of inhomogeneous regions in membranes. Discusses important methodological issues when using simulations to examine phenomena such as pore creation and permeation across membranes. Discusses progress recently achieved in modeling bacterial membranes. It will be a valuable resource for graduate students, researchers and instructors in biochemistry, biophysics, pharmacology, physiology, and computational biology.

Spectroscopy Of Biological Molecules Modern Trends

Author: P. Carmona
Publisher: Springer Science & Business Media
ISBN: 9780792346852
Size: 71.60 MB
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The 1997 European Conference on Spectroscopy of Biological Molecules (ECSBM) is the seventh in a biennial series of conferences devoted to the applications of molecular spectroscopy to biological molecules and related systems. The interest of these conferences rests mainly on the relationship between the structure and physiological activity of biological molecules and related systems of which these molecular species form part. This volume ofECSBM contains articles prepared by the invited lecturers and those making poster presentations at the seventh ECSBM. The reader will find mainly applications of vibrational spectroscopy to protein structure and dynamics, biomembranes, molecular recognition, nucleic acids and other biomolecules and biological systems containing specific chromophors. Biomedical applications of vibrational spectroscopy are expanding rapidly. On the other hand, a significant number of the papers describe applications of other methods, such as NMR, circular dichroism, optical absorption and fluorescence, X-ray absorption and diffraction and other theoretical methods. One aim has been to achieve a well balanced, critically comparative review of recent progress in the field of biomolecular structure, bonding and dynamics based on applications of the above spectroscopic methods. A great part of the contributions included in this volume are devoted to biomedical and biotechnological applications and provide a broadly based account of recent applicationS in this field. The content of this book has been organized in sections corresponding mainly to the different types of biological molecules investigated. This book includes also another section related to theoretical methods where MO calculations of vibrational frequencies dominate clearly the topic.

Molecular Simulation Studies In Material And Biological Sciences

Author: Kholmirzo Kholmurodov
Publisher: Nova Publishers
ISBN: 9781594546075
Size: 20.25 MB
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Computer molecular simulations of complex multi-particle systems play a fascinating role in fundamental physics, biochemical and life sciences. The chemical, pharmaceutical, materials and related industries - all share the computer molecular simulation methods. This book presents leading international research in this dynamic field.

Biomembrane Structures

Author: Parvez I. Haris
Publisher: IOS Press
ISBN: 9789051993233
Size: 49.80 MB
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Biological membranes play a significant role in a range of biological processes such as ion-transport and signal transduction. Over the years much effort has been devoted towards developing an understanding of biomembrane structure. The study of this subject is now reaching an important stage. This is because at last the full three-dimensional structure of certain membrane proteins is beginning to be resolved. In the past three-dimensional structures of membrane proteins were difficult to obtain as only two dimensional crystals were available. In recent years satisfactory crystals have been obtained and X-ray diffraction techniques have been applied. This has led to the three dimensional structures of the photosynthetic reaction centres, porins and more recently the structure of cytochrome oxidase. Of course not all membrane proteins are readily crystallisable and some are not even available in sufficient quantities to obtain the necessary crystals or to carry out biophysical experiments. In some cases e.g. the voltage-gated potassium ion channel membrane proteins their structure has been proposed mainly on the basis of molecular biology methods. This has prompted the search for alternative approaches for characterising biomembrane structure. Molecular biological studies are providing a wealth of information on a number of different membrane proteins. Combining the information derived from such studies with molecular modelling is becoming extremely useful for relating structure to function. Development of other approaches include synthesis and structure- function analysis of peptides corresponding to functionally important domains of membrane proteins. This book presents a series of Chapters discussing how a combination of molecular biological, biophysical and theoretical (molecular modelling) techniques are helping us to obtain a much clearer picture of biomembrane structure. After an introductory Chapter on the Principles of membrane Protein Structure, the book is divided into two sections; one dealing with crystallographic approaches and the other non-crystallographic approaches such as NMR, AFM, SPR and FTIR spectroscopy. Chapters dealing with the recently solved crystal structure of cytochrome oxidase and bacteriorhodopsin are presented. The book contains contributions from leading membrane scientists describing their latest studies. It provides an up to date coverage of the developments in the field of biomembranes with particular emphasis on membrane proteins.

Polymer Membranes Biomembranes

Author: Wolfgang Peter Meier
Publisher: Springer Science & Business Media
ISBN: 3642104789
Size: 26.56 MB
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Themulticomponentnatureofbiologicalmembranesandtheirintra- andextracel- lar interactions make direct investigations on the membrane structure and processes nearly impossible. Clearly, a better understanding of the membrane properties and the mechanisms determining membrane protein functions is crucial to the imp- mentation of biosensors, bioreactors and novel platforms for medical therapy. For this reason, the interest in model systems suitable for the construction and study of complex lipid/protein membrane architectures has increased steadily over the years. The classical portfolio of model membranes used for biophysical and - terfacial studies of lipid (bi)layers and lipid/protein composites includes Langmuir monolayers assembled at the water/air interface, (uni- and multi-lamellar) vesicles in bulk (liposomal) dispersion, bimolecular lipid membranes (BLMs), and various types of solid-supported membranes. All these have speci?c advantages but also suffer from serious drawbacksthat limit their technical applications. Polymer m- branes comprised of entirely synthetic or hybrid (synthetic polymer/biopolymer) block copolymersappeared to be an attractive alternative to the lipid-based models. Generally, the synthetic block copolymer membranes are thicker and more stable and the versatility of polymer chemistry allows the adoption of relevant properties for a wide range of applications. This volume provides a vast overview of the physico-chemical and synthetic - pectsofarti?cial membranes. Numerousmembranemodelsaredescribed, including their properties(i. e. swelling, drying, lateral mobility, stability, electrical conduct- ity, etc. ), advantages, and drawbacks. The potential applications of these models are discussed and supported by real examples. Chapter 1 summarizesmethodsfor the stabilizationof arti?cial lipid membranes.

Molecular Modeling Of Biomembrane Deformations The Role Of Lipids

Author: Eric R. May
Size: 61.98 MB
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ABSTRACT: Cellular transport processes such as endocytosis and exocytosis involve the budding of vesicles from the donor membrane (fission) and their integration into the membrane of the acceptor compartment (fusion). Both fission and fusion are energetically unfavorable, since they involve the formation of highly curved non-bilayer intermediates. Consequently, these processes do not occur spontaneously; they are under the strict control of specific proteins. In the classical paradigm of fission, membrane deformation was thought to be driven entirely by interactions between proteins. Evidence is now accumulating that these proteins do not act alone. They operate in concert with specific membrane lipids, such as phosphoinositides (PI), which localize in the region of deformation. It is of interest to understand the extent to which the localized phosphoinositides change the mechanical properties of biomembranes. In this work, a coarse grain molecular model is used to conduct molecular dynamics (MD) simulations of mixed lipid systems. The initial part of the work focuses on the verification of the molecular model by comparing simulation data to experimental phase transition data for mixed lipid systems containing dioleoyl phosphatidyle ethanolamine (DOPE), dioleoyl phosphatidic acid (DOPA) and lysophosphatidic acid (LPA). Also, the molecular geometries of the previously mentioned lipids are characterized and related the mechanisms driving the phase transitions. Additionally, MD simulations and analyses are performed on another mixed lipid system consisting of dipalmitoyl phosphatidyl choline (DPPC) and phosphatidylinositol-4-phosphate (PI4P). In this study two elastic parameters of the membrane are measured from the simulations, namely, the bending modulus and the coefficient of line tension between membrane domains of different composition.


Author: Lester Packer
Publisher: Academic Pr
Size: 49.31 MB
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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.