[PDF] Using Molecular Dynamics Simulations And Statistical Modeling To Explore Membrane Structure And Membrane Protein Interactions eBook

Author : Shushan He
Publisher :
Page : 111 pages
File Size : 17,34 MB
Release : 2018
Category :
ISBN :

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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
Page : 493 pages
File Size : 11,57 MB
Release : 2011-08-29
Category : Science
ISBN : 0080879705

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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
Page : 331 pages
File Size : 33,42 MB
Release : 2010-08-01
Category : Science
ISBN : 1849732159

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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.

Author :
Publisher : Elsevier
Page : 630 pages
File Size : 25,98 MB
Release : 2024-07-21
Category : Science
ISBN : 0443295670

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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 :
Page : 177 pages
File Size : 49,47 MB
Release : 2015
Category :
ISBN : 9781321702125

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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
Page : 274 pages
File Size : 11,28 MB
Release : 2016-12-05
Category : Science
ISBN : 1782624902

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Exploring current themes in modern computational and membrane protein biophysics, this book is ideal for researchers in computational chemistry and computational biophysics.

Author : Kayla Sapp
Publisher :
Page : 96 pages
File Size : 49,47 MB
Release : 2016
Category : Langevin equations
ISBN :

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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 : Christophe Chipot
Publisher : Springer Science & Business Media
Page : 528 pages
File Size : 20,93 MB
Release : 2007-01-08
Category : Language Arts & Disciplines
ISBN : 3540384472

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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 : Siddhartha Roy
Publisher : Royal Society of Chemistry
Page : 399 pages
File Size : 18,89 MB
Release : 2020-12-14
Category : Science
ISBN : 1839160500

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New genomic information has revealed the crucial role that protein–protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein–Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.

Author : Andreas Kukol
Publisher : Humana Press
Page : 474 pages
File Size : 46,88 MB
Release : 2017-04-30
Category : Science
ISBN : 9781493954919

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Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.