Download or read book A Novel Computational Method Incorporates the Molecular Details of Transmembrane Proteins Into the Quantitative Evaluation of Lipid protein Interactions and Their Mechanistic Role written by Sayan Mondal and published by . This book was released on 2014 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physiological function requires modulated communication across the cell membrane, mediated in part by proteins that span the membrane with multiple transmembrane segments (TM), e.g., 7-TM receptors (GPCRs), transporters, and ion channels. While the effects of these proteins propagate across multiple spatial and temporal scales to cause physiological responses, they themselves are activated and modulated at the molecular scale. For example, the activation of thve 7-TM receptors has been shown to occur via changes in the conformation of the molecule, predominantly a movement of particular TMs, viz. TM5 and TM6. This dissertation evolves a quantitative understanding of how such molecular mechanisms of multi-TM proteins involve the participation of their membrane environment. The cost of the adaptation of the membrane to the protein is evaluated in terms of the energy cost for membrane remodeling near the protein. In previous studies (Huang, Biophysical J 1986; Nielsen et al., Biophysical J 1999), this energy cost could explain experimental observations of the role of the membrane in the function of model single-TM peptides like gramicidin A ion channels, at a quantitative level. To quantify the energetics for multi-TM proteins taking into account their relevant molecular details, a new hybrid Continuum-Molecular Dynamics (CTMD) method is developed. This novel method uses the experimentally validated continuum approach for quantifying the energetics of membrane remodeling near the protein, but in combination with a molecular description of the lipid-protein interface from cognate Molecular Dynamics simulations. Thus, it takes into account the structural and dynamic conformational properties of multi-TM proteins, making it possible to quantitatively investigate the role of the membrane in their molecular mechanisms. This is illustrated for the activation and oligomerization of 7-TM receptors, and the substrate transport of neurotransmitter transporters. The illustrative applications reveal specific molecular regions involved in energetically significant interactions with the membrane, and demonstrate that local, energetically costly interactions are mechanistically important. The applications show as well how these interactions differ for lipid compositions having different physico-chemical properties, thus placing the mechanistic role of the membrane in the context of the compositional heterogeneity of the cell membrane.
Download or read book Lipid Protein Interactions written by Jörg H. Kleinschmidt and published by Humana Press. This book was released on 2013-02-14 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological membranes are the essential structuring elements of all living cells. Many enzymatic reactions take place at the membrane-water interface. To gain detailed insight into membrane properties, it is therefore of great importance to understand the complex nature of the interactions of membrane proteins with lipids. Lipid-Protein Interactions: Methods and Protocols provides a selection of protocols to examine protein-lipid interactions, membrane and membrane protein structure, how membrane proteins affect lipids and how they are in turn affected by the lipid bilayer and lipid properties. The methods described here are all actively used, complementary, and necessary to obtain comprehensive information about membrane structure and function. They include label-free approaches, imaging techniques and spectroscopic methodologies. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Lipid-Protein Interactions: Methods and Protocols seeks to serve both professional and novices with its wide range of the methods frequently used in this area of research.
Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Download or read book Lipid mediated Protein Signaling written by Daniel G.S. Capelluto and published by Springer Science & Business Media. This book was released on 2013-06-17 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides the most updated information of how membrane lipids mediate protein signaling from studies carried out in animal and plant cells. Also, there are some chapters that go beyond and expand these studies of protein-lipid interactions at the structural level. The book begins with a literature review from investigations associated to sphingolipids, followed by studies that describe the role of phosphoinositides in signaling and closing with the function of other key lipids in signaling at the plasma membrane and intracellular organelles.
Download or read book Peptide Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction
Download or read book Protein Protein Interaction Networks written by Stefan Canzar and published by Humana. This book was released on 2019-10-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores techniques that study interactions between proteins in different species, and combines them with context-specific data, analysis of omics datasets, and assembles individual interactions into higher-order semantic units, i.e., protein complexes and functional modules. The chapters in this book cover computational methods that solve diverse tasks such as the prediction of functional protein-protein interactions; the alignment-based comparison of interaction networks by SANA; using the RaptorX-ComplexContact webserver to predict inter-protein residue-residue contacts; the docking of alternative confirmations of proteins participating in binary interactions and the visually-guided selection of a docking model using COZOID; the detection of novel functional units by KeyPathwayMiner and how PathClass can use such de novo pathways to classify breast cancer subtypes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary hardware- and software, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Protein-Protein Interaction Networks: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in learning more about this evolving field.
Download or read book Allosteric Modulation of G Protein Coupled Receptors written by Robert Laprairie and published by Academic Press. This book was released on 2022-02-05 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Allosteric Modulation of G Protein-Coupled Receptors reviews fundamental information on G protein-coupled receptors (GPCRs) and allosteric modulation, presenting original research in the area and collectively providing a comprehensive description of key issues in GPCR allosteric modulation. The book provides background on core concepts of molecular pharmacology while also introducing the most important advances and studies in the area. It also discusses key methodologies. This is an essential book for researchers and advanced students engaged in pharmacology, toxicology and pharmaceutical sciences training and research. Many of the GPCR-targeted drugs released in the past decade have specifically worked via allosteric mechanisms. Unlike direct orthosteric-acting compounds that occupy a similar receptor site to that of endogenous ligands, allosteric modulators alter GPCR-dependent signaling at a site apart from the endogenous ligand. Recent methodological and analytical advances have greatly improved our ability to understand the signaling mechanisms of GPCRs. We now know that allostery is a common regulatory mechanism for all GPCRs and not – as we once believed – unique to a few receptor subfamilies. Introduces background on core concepts of molecular pharmacology, including statistical analyses, non-linear regression, complex models and GPCR-dependent signal transduction as they relate to allosteric modulation Discusses critical advances and landmark studies, including discoveries in the area of GPCR allosteric modulation, which are reviewed for their importance in positive and negative regulation, protein-protein interactions, and small molecule drug discovery Includes key methodologies used to study allosteric modulation at the in silico, in vitro, and in vivo levels of drug discovery and characterization
Download or read book Computational Biophysics of Membrane Proteins written by Carmen Domene and published by Royal Society of Chemistry. This book was released on 2016-11-30 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring current themes in modern computational and membrane protein biophysics, this book presents a comprehensive account of the fundamental principles underlying different methods and techniques used to describe the intriguing mechanisms by which membrane proteins function. The book discusses the experimental approaches employed to study these proteins, with chapters reviewing recent crucial structural advances that have allowed computational biophysicists to discern how these molecular machines work. The book then explores what computational methods are available to researchers and what these have taught us about three key families of membrane proteins: ion channels, transporters and receptors. The book is ideal for researchers in computational chemistry and computational biophysics.
Download or read book Current Topics in Membranes and Transport written by and published by Academic Press. This book was released on 1974-04-10 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes and Transport
Download or read book Mechanisms of Insulin Action written by Alan R. Saltiel and published by Springer Science & Business Media. This book was released on 2007-10-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: More than 18 million people in the United States have diabetes mellitus, and about 90% of these have the type 2 form of the disease. This book attempts to dissect the complexity of the molecular mechanisms of insulin action with a special emphasis on those features of the system that are subject to alteration in type 2 diabetes and other insulin resistant states. It explores insulin action at the most basic levels, through complex systems.
Download or read book The Biophysics of Cell Membranes written by Richard M. Epand and published by Springer. This book was released on 2017-09-25 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the modulation of biological membranes by specific biophysical properties. The readers are introduced to emerging biophysical approaches that mimick specific states (like membrane lipid asymmetry, membrane curvature, lipid flip-flop, lipid phase separation) that are relevant to the functioning of biological membranes. The first chapter describes innovative methods to mimic the prevailing asymmetry in biological membranes by forming asymmetrical membranes made of monolayers with different compositions. One of the chapters illustrates how physical parameters, like curvature and elasticity, can affect and modulate the interactions between lipids and proteins. This volume also describes the sensitivity of certain ion channels to mechanical forces and it presents an analysis of how cell shape is determined by both the cytoskeleton and the lipid domains in the membrane. The last chapter provides evidence that liposomes can be used as a minimal cellular model to reconstitute processes related to the origin of life. Each topic covered in this volume is presented by leading experts in the field who are able to present clear, authoritative and up-to-date reviews. The novelty of the methods proposed and their potential for a deeper molecular description of membrane functioning are particularly relevant experts in the areas of biochemistry, biophysics and cell biology, while also presenting clear and thorough introductions, making the material suitable for students in these fields as well.
Download or read book Molecular Epidemiology written by Paul A. Schulte and published by Academic Press. This book was released on 2012-12-02 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will serve as a primer for both laboratory and field scientists who are shaping the emerging field of molecular epidemiology. Molecular epidemiology utilizes the same paradigm as traditional epidemiology but uses biological markers to identify exposure, disease or susceptibility. Schulte and Perera present the epidemiologic methods pertinent to biological markers. The book is also designed to enumerate the considerations necessary for valid field research and provide a resource on the salient and subtle features of biological indicators.
Download or read book Cell Boundaries written by Stephen H White and published by Garland Science. This book was released on 2021-12-31 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: The central themes of Cell Boundaries concern the structural and organizational principles underlying cell membranes, and how these principles enable function. By building a biological and biophysical foundation for understanding the organization of lipids in bilayers and the folding, assembly, stability, and function of membrane proteins, the book aims to broaden the knowledge of bioscience students to include the basic physics and physical chemistry that inform us about membranes. In doing so, it is hoped that physics students will find familiar territory that will lead them to an interest in biology. Our progress toward understanding membranes and membrane proteins depends strongly upon the concerted use of both biology and physics. It is important for students to know not only what we know, but how we have come to know it, so Cell Boundaries endeavours to bring out the history behind the central discoveries, especially in the early chapters, where the foundation is laid for later chapters. Science is far more interesting if, as students, we can appreciate and share in the adventures—and misadventures—of discovering new scientific knowledge. Cell Boundaries was written with advanced undergraduates and beginning graduate students in the biological and physical sciences in mind, though this textbook will likely have appeal to researchers and other academics as well. Highlights the history of important central discoveries Early chapters lay the foundation for later chapters to build on, so knowledge is amassed High-quality line diagrams illustrate key concepts and illuminate molecular mechanisms Box features and spreads expand on topics in main text, including histories of discoveries, special techniques, and applications
Download or read book Protein Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.
Download or read book Molecular Diagnostics Promises and Possibilities written by Mousumi Debnath and published by Springer Science & Business Media. This book was released on 2010-01-29 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt: A rapid development in diverse areas of molecular biology and genetic engineering resulted in emergence of variety of tools. These tools are not only applicable to basic researches being carried out world over, but also exploited for precise detection of abnormal conditions in plants, animals and human body. Although a basic researcher is well versed with few techniques used by him/her in the laboratory, they may not be well acquainted with methodologies, which can be used to work out some of their own research problems. The picture is more blurred when the molecular diagnostic tools are to be used by physicians, scientists and technicians working in diagnostic laboratories in hospitals, industry and academic institutions. Since many of them are not trained in basics of these methods, they come across several gray areas in understanding of these tools. The accurate application of molecular diagnostic tools demands in depth understanding of the methodology for precise detection of the abnormal condition of living body. To meet the requirements of a good book on molecular diagnostics of students, physicians, scientists working in agricultural, veterinary, medical and pharmaceutical sciences, it needs to expose the reader lucidly to: Give basic science behind commonly used tools in diagnostics Expose the readers to detailed applications of these tools and Make them aware the availability of such diagnostic tools The book will attract additional audience of pathologists, medical microbiologists, pharmaceutical sciences, agricultural scientists and veterinary doctors if the following topics are incorporated at appropriate places in Unit II or separately as a part of Unit-III in the book. Molecular diagnosis of diseases in agricultural crops Molecular diagnosis of veterinary diseases. Molecular epidemiology, which helps to differentiate various epidemic strains and sources of disease outbreaks. Even in different units of the same hospital, the infections could be by different strains of the same species and the information becomes valuable for infection control strategies. Drug resistance is a growing problem for bacterial, fungal and parasitic microbes and the molecular biology tools can help to detect the drug resistance genes without the cultivation and in vitro sensitivity testing. Molecular diagnostics offers faster help in the selection of the proper antibiotic for the treatment of tuberculosis, which is a major problem of the in the developing world. The conventional culture and drug sensitivity testing of tuberculosis bacilli is laborious and time consuming, whereas molecular diagnosis offers rapid drug resistant gene detection even from direct clinical samples. The same approach for HIV, malaria and many more diseases needs to be considered. Molecular diagnostics in the detection of diseases during foetal life is an upcoming area in the foetal medicine in case of genetic abnormalities and infectious like TORCH complex etc. The book will be equally useful to students, scientists and professionals working in the field of molecular diagnostics.
Download or read book Approximate Analytical Methods for Solving Ordinary Differential Equations written by T.S.L Radhika and published by CRC Press. This book was released on 2014-10-31 with total page 584 pages. Available in PDF, EPUB and Kindle. Book excerpt: Approximate Analytical Methods for Solving Ordinary Differential Equations (ODEs) is the first book to present all of the available approximate methods for solving ODEs, eliminating the need to wade through multiple books and articles. It covers both well-established techniques and recently developed procedures, including the classical series solution method, diverse perturbation methods, pioneering asymptotic methods, and the latest homotopy methods. The book is suitable not only for mathematicians and engineers but also for biologists, physicists, and economists. It gives a complete description of the methods without going deep into rigorous mathematical aspects. Detailed examples illustrate the application of the methods to solve real-world problems. The authors introduce the classical power series method for solving differential equations before moving on to asymptotic methods. They next show how perturbation methods are used to understand physical phenomena whose mathematical formulation involves a perturbation parameter and explain how the multiple-scale technique solves problems whose solution cannot be completely described on a single timescale. They then describe the Wentzel, Kramers, and Brillown (WKB) method that helps solve both problems that oscillate rapidly and problems that have a sudden change in the behavior of the solution function at a point in the interval. The book concludes with recent nonperturbation methods that provide solutions to a much wider class of problems and recent analytical methods based on the concept of homotopy of topology.
Download or read book Computational Pharmaceutics written by Defang Ouyang and published by John Wiley & Sons. This book was released on 2015-07-20 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.
