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Author: Shushan He
Publisher:
ISBN:
Category :
Languages : en
Pages : 111
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Book Description
The structure of cellular membranes gives rise to important biological phenomena, and understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step toward unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. In this dissertation we focus on the spatial organization and compositional heterogeneity of model membrane systems and their interaction with small, biologically relevant peptides. I employed both coarse-grained and atomistic molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol, as well as to sample the configurational space of peptide-membrane interactions. I investigate the mechanisms controlling membrane spatial heterogeneity and membrane protein interaction. This work yields important new insight into both the structural properties of lipid bilayer systems with spatial and compositional heterogeneity at vastly different length scales, which has prompted numerous publications in the field seeking for a plausible mechanism. This work will also provide perspectives on configurations of the PAP248-286 peptide upon interacting with membranes, which, despite its importance for human health, has not received as much attention from the research community as other amyloid-forming peptides. In this wide-open field such simulations will have significant scientific impact.
Author: Shushan He
Publisher:
ISBN:
Category :
Languages : en
Pages : 111
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Book Description
The structure of cellular membranes gives rise to important biological phenomena, and understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step toward unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. In this dissertation we focus on the spatial organization and compositional heterogeneity of model membrane systems and their interaction with small, biologically relevant peptides. I employed both coarse-grained and atomistic molecular dynamics simulations to study the composition phase diagram of a quaternary mixture of phospholipids and cholesterol, as well as to sample the configurational space of peptide-membrane interactions. I investigate the mechanisms controlling membrane spatial heterogeneity and membrane protein interaction. This work yields important new insight into both the structural properties of lipid bilayer systems with spatial and compositional heterogeneity at vastly different length scales, which has prompted numerous publications in the field seeking for a plausible mechanism. This work will also provide perspectives on configurations of the PAP248-286 peptide upon interacting with membranes, which, despite its importance for human health, has not received as much attention from the research community as other amyloid-forming peptides. In this wide-open field such simulations will have significant scientific impact.
Author: V. Sundararajan
Publisher: Academic Press
ISBN: 0080879705
Category : Science
Languages : en
Pages : 493
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Book Description
Current Topics in Membranes provides a systematic, comprehensive, and rigorous approach to specific topics relevant to the study of cellular membranes. Each volume is a guest edited compendium of membrane biology. *Discusses the current stat of electrostatics in biomolecular simulations and future directions *Includes information on time and length scales in lipid bilayer simulations *Includes a chapter on the nature of lipid rafts
Author: Mark S P Sansom
Publisher: Royal Society of Chemistry
ISBN: 1849732159
Category : Science
Languages : en
Pages : 331
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Book Description
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.
Author:
Publisher: Elsevier
ISBN: 0443295670
Category : Science
Languages : en
Pages : 630
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Book Description
Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more. Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics. Explore the state-of-the-art of lipid membrane asymmetry Covers experimental, theoretical, and computational techniques to create and characterize asymmetric lipid membranes Teaches how these kinds of approaches create and characterize laterally inhomogeneous membranes
Author: Benjamin D. Madej
Publisher:
ISBN: 9781321702125
Category :
Languages : en
Pages : 177
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Book Description
Cellular membranes are incredibly complex structures composed of diverse biomolecules including lipids, proteins, and other molecules. Cellular membranes are important because they allow for the transfer of molecules and chemical signals in and out of cells. The structure of membranes and membrane proteins is difficult to determine through experiments. Membrane structure is also highly dynamic and depends on the mixture of molecular components. While the membrane is usually in the liquid-disordered phase, other local membrane assemblies have been observed. It is challenging to predict the permeation of pharmaceutical compounds through the membrane. Molecular dynamics (MD) is a computational method that allows for the study of membrane motions and drug interactions. Based on a chemical model of molecules and Newton's equations of motion, it is possible to predict the dynamics of molecules on a computer. However, in order to simulate new molecules, it is necessary to refine an appropriate force field that models the chemical interactions of the molecules. A new force field was developed for lipids, an essential membrane component in the Amber MD software package. This force field was parameterized with experimental data and quantum mechanical calculations on individual chemical components of the lipid molecule. Afterwords, parameters were validated against available membrane structural data. Parameters have been developed for a set of glycerophospholipids and cholesterol. Molecular dynamics simulations of lipid membranes with the new parameters have accurately predicted membrane structural properties. With an accurate model of lipid membranes, it is now possible to examine complex membrane dynamics. Permeation of small molecules across the membrane is especially interesting in the pharmaceutical industry. Using the inhomogenous solubility-diffusion model it is possible to predict small-molecule permeability across a membrane from potential of mean force calculations. A constrained molecular dynamics algorithm was implemented in Amber for this task. The constraint implementation may be optimized to run on graphics processing units (GPU). This dissertation marks the first expanded lipid force field in Amber for accurate membrane simulations. It also marks the implementation of a accelerated general constraint methods in Amber.
Author: Carmen Domene
Publisher: Royal Society of Chemistry
ISBN: 1782624902
Category : Science
Languages : en
Pages : 274
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Book Description
Exploring current themes in modern computational and membrane protein biophysics, this book is ideal for researchers in computational chemistry and computational biophysics.
Author: Robert B. Gennis
Publisher: Springer Science & Business Media
ISBN: 1475720653
Category : Science
Languages : en
Pages : 549
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Book Description
New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermody namics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases, the availability of texts in active research areas should help stimulate the creation of new courses.
Author: Christophe Chipot
Publisher: Springer Science & Business Media
ISBN: 3540384472
Category : Language Arts & Disciplines
Languages : en
Pages : 528
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Book Description
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.
Author: Kayla Sapp
Publisher:
ISBN:
Category : Langevin equations
Languages : en
Pages : 96
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Book Description
The structure of the membrane gives rise to important biological phenomena. In this dissertation we focus on the shape of the membrane and its interactions through two different coupling schemes to membrane bound proteins. We develop a model based on the continuum description of the membrane that is used to investigate height-coupled and curvature-coupled membrane-protein systems. For these systems we use coupled Langevin equations to model the dynamics for the Fourier modes of the membrane and protein position in the xy-plane. We investigate similarities and differences in these two coupling schemes in how they alter membrane fluctuations, protein-protein interactions, and lateral protein diffusion. We further expand on previous dynamic membrane-protein models by deriving from the Fokker-Planck formalism a consistent Langevin equations that accurately models the dynamics of systems with protein diffusing along the membrane surface. We investigate how the model differs from previous in the discussion of later protein diffusion.
Author: Ronald J. Clarke
Publisher: John Wiley & Sons
ISBN: 1118858808
Category : Science
Languages : en
Pages : 488
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Book Description
Describes experimental methods for investigating the function of pumps, channels and transporters Covers new emerging analytical methods used to study ion transport membrane proteins such as single-molecule spectroscopy Details a wide range of electrophysiological techniques and spectroscopic methods used to analyze the function of ion channels, ion pumps and transporters Covers state-of-the art analytical methods to study ion pumps, channels, and transporters, and where analytical chemistry can make further contributions
