Download or read book Phase and Phase transition Properties of Mono and Diglyceride Lipid Bilayers Investigated Using Molecular Dynamics Simulations written by Monika Laner and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural Behavior of Free Versus Supported Ternary Lipid Bilayer Membranes written by Holden Timothy Ranz and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Ternary lipid bilayer systems assembled from mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol have been studied using coarse-grained molecular dynamics at biologically relevant temperatures (280 K to 310 K), which fall between the chain melting temperatures of each pure lipid component. Free lipid bilayers were simulated using the MARTINI model (Stage I) and a variant with water-water interactions reduced to 76% (Stage II). The latter was subsequently used for preparing supported lipid bilayer simulations (Stage III). Clustering of like lipids was observed, but the simulation timescale did not yield larger phase-separated domains as expected for many systems. However, several critical phase transitions were elucidated by comparing static and dynamic bilayer properties. Such properties include bilayer thicknesses, lateral diffusion coefficients of head groups, and lipid chain order parameters. Bilayer thickness fell within the expected range of liquid/gel phase behavior, and order parameters had semi-quantitative agreement with NMR experiments. Diffusion coefficients had some qualitative agreement with data from pfg-NMR measurements when scaled up by a factor of 10. A solid support generally induced ordering within the bilayer, but at 310 K the inner-water region was often comprised of ordered layers and disordered particles, resulting in non-planar bilayer conformations.
Download or read book A Comparison of Phase Transition Properties of Supported Phospholipid Mono and Bilayers written by Sennur Turgut and published by . This book was released on 2008 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Advances in Planar Lipid Bilayers and Liposomes written by A. Ottova-Leitmannova and published by Gulf Professional Publishing. This book was released on 2005-09 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lipid bilayer is central to life, as all living organisms possess a lipid bilayer structure, thereby underlying the lipid bilayer principle of biomembranes. The lipid bilayer principle and its applications are the main theme of this new book series. This new series on bilayer lipid membranes (BLMs and liposomes) include invited chapters on a broad range of topics, from theoretical investigations, specific studies, experimental methods, to practical applications. Written for newcomers, experienced scientists, and those who are not familiar with these specific research areas, the Series covers all aspects of lipid bilayer investigations, both fundamental and applied. * Covers a broad range of topics ranging from theoretical research, specific studies, experimental methods, to practical applications * Authoritative timely reviews by experts in this field * Indispensable source of information for new scientists
Download or read book In celebration of women in science Lipids membranes and membranous organelles written by Elena G. Govorunova and published by Frontiers Media SA. This book was released on 2023-05-05 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Theoretical and Computational Studies of the Lateral Phases on a Multicomponent Lipid bilayer Surface written by Yongtian Luo and published by . This book was released on 2019 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lipid-bilayer membrane is the fundamental structure of a cell plasma membrane and has been largely studied by biophysical experiments, theoretical modeling and computer simulations. Two major aspects of lipid bilayer morphologies are studied, namely lateral phase separation and pattern formation (spatial organization of lipid molecules), and shape change or deformation of the membrane (undulation of the surface). In this dissertation, I apply theoretical modeling, analytical and numerical computation as well as molecular simulation to study the lateral phases on the surface of a multicomponent lipid bilayer, which is able to stay in a homogeneous state, phase separate, or transform into heterogeneous states including modulated phases and microemulsions. The focal point is a lipid-bilayer vesicle of finite size and spherical topology. I calculate phase diagrams which reveal the effects of intrinsic finite sizes of vesicles on their surface pattern and lateral phase generation. I also calculate the structure factor of vesicles, which is measured by scattering signals, and theoretically develop an approximate model-independent interconversion between the three-dimensional signal and the two-dimensional structure factor of planar membranes, and I also stress the finite size effect in this relation. It is also observed that the lipid domain formation is coupled with membrane curvature distribution on the surface. I apply the coupling through domain bending properties, and create phase diagrams in which changing membrane mechanical properties can vary the lateral phases on a vesicle surface. In addition to the aforementioned continuum modeling, I also utilize coarse-grained molecular dynamics simulation to explore the phase behavior of asymmetric lipid bilayers consisting of a phase-separating leaflet and a homogeneous leaflet, in which the former would induce a tendency of phase separation in the latter. The molecular simulation, which keeps a record of each lipid molecule, could be a more biologically relevant model of plasma membranes.
Download or read book Molecular Simulations of Lipid Bilayers and Membrane Helices Interactions written by Ayelet Benjamini and published by . This book was released on 2013 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work we use mesoscopic simulation to investigate the short and medium range interaction of transmembrane helices. First, we develop a coarse-grained model of a generic transmembrane [alpha]-helix. We use the geometry constraints of an [alpha]-helix, along with a set of homogeneous hydrophobic beads. We discuss the reasoning behind this modeling and why various other plausible models have failed in describing the short-range interactions of transmembrane helices. We then show the effect of hydrophobic mismatch on these model helices. The tilt angle of a single helix is affected by its hydrophobic mismatch with the surrounding bilayer. We show that the hydrophobic mismatch, via its effect on the tilt angle, has a crucial effect on the cross angle of two packed transmembrane helices as well. We further show the effect of hydrophobic mismatch on the potential of mean force between the helices as well as on the thickness and tilt angle of the lipids surrounding the helices. We introduce a class of especially long helices, termed super-positive mismatched helices, to which the response of the lipids differs and discuss the origin of this behavior. These coarse-grained simulations are performed using the Dissipative Particle Dynamics (DPD) scheme Performing large time and length scale simulations using this scheme is highly CPU-time consuming. To enhance our simulation capabilities we develop a novel, massively parallel simulation algorithm. We introduce this algorithm and the original concepts we developed for parallelizing the DPD scheme. We show that this novel approach provides up to 30 times speed up on a Graphical Processing Unit (GPU) over the non-parallel CPU version. Finally, we use our parallel algorithm to perform simulation on a large time and length scale system. We investigate the effect of Cholesterol on the bending rigidity of lipid bilayers and show the effect of a phase transition on the bending modulus. Extracting the bending modulus from simulation requires a large system that enables long-range height fluctuations. Using a fast, parallel simulation algorithm for such a task is therefore crucial.
Download or read book Molecular Dynamics Studies of Lipid Monolayer and Bilayer Systems written by Bin Liu and published by . This book was released on 2016 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lipids are a crucial ingredient of biomembranes in cells, and they play a pivotal role in many chemical and biological processes. Lipid based structures, such as lipid monolayers and lipid bilayers, both natural and artificial, are gaining their importance and popularity in drug delivery. In this thesis, our main interest is on using molecular modeling and atomistic molecular dynamics simulations to study lipid monolayers and bilayers, and their physical properties and interactions with an antibiotic molecule called daptomycin. This thesis is composed of the research results from two projects. The first project focuses on an atomistic molecular dynamcis study of lipid Langmuir monolayers composed of both pure zwitterionic dipalmitoylphosphatidylcholine (DPPC) and a mixture of DPPC and cationic cetyltrimethylammonium bromide (CTAB). The cationic CTAB lipids have been found to have significant condensing effect on the DPPC / CTAB monolayers, i.e., at the same surface tension or surface pressure, monolayers with higher CTAB molar fraction have smaller area per lipid. With this condensing effect, the DPPC / CTAB monolayers are also able to achieve negative surface tension without introducing buckling into the monolayer structure. The condensing effect is caused by the interplay between the cationic CTAB headgroups and the zwitterionic phosphatidylcholine (PC) headgroups which has electrostatic origin. Moreover, detailed analysis of the structural properties of the monolayers, such as the density profile analysis, hydrogen bonding analysis, chain order parameter calculations and radial distribution function calculations were also performed for better understanding of cationic DPPC/CTAB monolayers. A chapter is dedicated to the discussion of the mean and Gaussian curvatures of the pure DPPC and DPPC/CTAB mixture monolayers. In the second project, MD simulations were employed to study the atomistic details of the antimicrobial activities of daptomycin, a cyclic anionic lipopeptide which treats infections caused by Gram-positive bacteria, with emphasis on its interactions with a model bacteria membrane. Despite having itself a net negative charge, it is selective against negatively charged bacterial membranes. It has been established that daptomycin's antibiotic activity is based on targeting the bacterial membranes and that this antibacterial activity depends on calcium ions. Importantly, however, both the precise role of ions and the physical mechanisms responsible for daptomy-cin's action remain poorly understood. We investigate these issues using three types of molecular dynamics simulations: free energy calculations for a single daptomycin, unbiased simulations for daptomycin tetramers and micellation of daptomycin both in the absence and presence of calcium ions.
Download or read book Liposomes Lipid Bilayers and Model Membranes written by Georg Pabst and published by CRC Press. This book was released on 2014-03-04 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a result of their unique physical properties, biological membrane mimetics, such as liposomes, are used in a broad range of scientific and technological applications. Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application describes state-of-the-art research and future directions in the field of membranes, which has evo
Download or read book How Solid Substrates Affect a Lipid Bilayer written by Chenyue Xing and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We use Molecular Dynamics (MD) simulations to investigate how solid substrates interact with a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer and how substrates affect the lipid membrane structurally and dynamically. Supported lipid bilayers are extensively used in experiments as a simplified model for cell membranes. Few simulations of supported bilayers have been performed. We use the MARTINI coarse-grained model to study the supported bilayer computationally. When a lipid bilayer is deposited on the solid substrate, the undulation of the proximal leaflet is suppressed to a higher extent than that of the distal leaflet. Properties of the bilayer including density profiles and lateral mobility exhibit heterogeneity. The proximal leaflet is ordered under the influence of a smooth surface, while the distal leaflet remains the similar to the leaflets in a free-standing bilayer. The lateral pressure profile of the supported bilayer is also different from that of a free-standing bilayer. Membrane proteins undergo undesired conformational changes due to the change in the lateral pressure profile. We study in particular the high local pressure in the proximal leaflet and estimate the interfacial energy associated with it. The interfacial energy falls in the range of activation energy barriers of the large mechanosensative channel (MscL) and may contribute to the opening of MscL without external pressure. Experiencing the strong inwards tension, the proximal leaflet prefers a smaller area per molecule than the distal leaflet and free-standing bilayers. We employ the umbrella sampling technique to calculate the potential of mean force (PMF) of lipid translocation. The free energy difference given by the PMF of various supported bilayer systems indicate that the proximal leaflet needs more lipids than the distal leaflet. The equilibrium density imbalance between two leaflets in the supported bilayer is roughly 4-7%. In addition, the equilibrium area per molecule of the proximal leaflet is estimated to be around 58 Å2, about 4 Å2 smaller than that of the free-standing bilayer. The lipid flip-flop rate in a supported bilayer with the same number of lipids in both leaflets is higher than in the free-standing bilayer, because the energy barrier of flip-flop is lowered by a few kBT.
Download or read book Permeability and Stability of Lipid Bilayers written by E. Anibal Disalvo and published by CRC Press. This book was released on 2017-12-14 with total page 298 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a comprehensive and coherent picture of how molecules diffuse across a liquid that is, on average, only two molecules thick. It begins by characterizing bilayers structurally, using X-ray diffraction, and then mechanically by measuring elastic moduli and mechanisms of failure. Emphasis is placed on the stability and mechanical properties of plant membranes that are subject to very large osmotic and thermal stresses. Using this information, the transport of molecules of increasing complexity across bilayers is analyzed.
Download or read book The Effects of Solid Substrates on Thermodynamics of Lipid Membranes written by Asma Poursoroush and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The phase behavior of lipid membrane next to solid substrates isinvestigated numerically using molecular dynamics simulations of a coarse- grained implicit-solvent model. We particularly investigated the effect of the strength of the adhesion of the lipids on the substrate on the gel-fluid phase transition. The behavior of the proximal leaflet of the lipid bilayer can be dramatically different from that of the distal leaflet, particularly for large adhesion strengths. In the gel phase, the lipids of the proximal leaflet are uniformly in the gel phase while the lipids of the distal leaflet are spatially distributed in coexisting gel and fluid domains. We have shown that the difference in the behavior of the two leaflets is due to the difference in their lipid densities. The different lipid densities are the result of enhanced lipid translocation from the distal leaflet to the proximal leaflet due to the attractive substrate.
Download or read book Coupling and Clustering in Molecular Dynamics Simulation Studies of Lipid Membrane Biophysics written by Michael David Weiner and published by . This book was released on 2018 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: The plasma membrane defines a eukaryotic cell, separating the cell's interior from its surroundings. Structurally, the plasma membrane is a lipid bilayer, composed of numerous different lipids and proteins. A biophysical approach to understanding this system examines the behavior of the liquid crystal phases of the membrane's lipids. In particular, membrane rafts, regions with distinct physical properties, may be studied in model membranes using coexisting liquid phases containing as few as three lipid components. The findings described in this dissertation employ Molecular Dynamics simulations, computational models of the physics of interacting atoms and molecules, to explore the biophysical chemistry of lipid bilayers. Coarse-grained Molecular Dynamics simulations use simplified molecular models, which makes reproducing spontaneous demixing into coexisting liquid phases computationally feasible. The first study presented uses coarse-grained simulations to examine coupling between the two leaflets of a model membrane. While most publications report alignment of like domains, this study shows that lengthening the acyl chains of the high-melting-temperature phospholipid component or increasing the cholesterol concentration yields an alignment of unlike domains, accompanied by the appearance of a significant presence of cholesterol at the bilayer midplane, between the leaflets. The second study takes a different approach to leaflet coupling, engaging in atomistic simulations of compositionally asymmetric bilayers. Different lipids are present in each leaflet of the plasma membrane, so an asymmetric composition offers a more physiological model. The work reveals that even a single-phase leaflet is coupled to a phase-separated leaflet, as it adopts slightly different physical properties in the regions interacting with different domains. This finding suggests that transmembrane communication through coupling can occur in cells. Finally, the third study considers the role of ions in clusters of phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid that makes up a small fraction of the plasma membrane but plays an outsize role in cell signaling and the retrovirus lifecycle. It confirms experimental evidence that clusters form in the presence of divalent cations but not monovalent ones and examines the interaction of ions and lipids and the impact on the lipids' physical properties.
Download or read book Protein Lipid Interactions written by C.Reyes Mateo and published by Springer Science & Business Media. This book was released on 2008-09-30 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological membranes have long been identified as key elements in a wide variety of cellular processes including cell defense communication, photosynthesis, signal transduction, and motility; thus they emerge as primary targets in both basic and applied research. This book brings together in a single volume the most recent views of experts in the area of protein–lipid interactions, providing an overview of the advances that have been achieved in the field in recent years, from very basic aspects to specialized technological applications. Topics include the application of X-ray and neutron diffraction, infrared and fluorescence spectroscopy, and high-resolution NMR to the understanding of the specific interactions between lipids and proteins within biological membranes, their structural relationships, and the implications for the biological functions that they mediate. Also covered in this volume are the insertion of proteins and peptides into the membrane and the concomitant formation of definite lipid domains within the membrane.
Download or read book Methods in Membrane Lipids written by Alex M. Dopico and published by Springer Science & Business Media. This book was released on 2007-08-30 with total page 1265 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a compendium of methodologies for the study of membrane lipids, varying from traditional lab bench experimentation to computer simulation and theoretical models. The volume provides a comprehensive set of techniques for studying membrane lipids with a strong biophysical emphasis. It compares the various available techniques including the pros and cons as seen by the experts.
Download or read book Advances in Planar Lipid Bilayers and Liposomes written by A. Leitmannova Liu and published by Elsevier. This book was released on 2011-08-09 with total page 441 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 5 presents recent research on both planar lipid bilayers and liposomes based on their historic and experimental realization. Advances in Planar Lipid Bilayers and Liposomes, Volume 5, continues to include invited chapters on a broad range of topics, covering both main arrangements of the reconstituted system, namely planar lipid bilayers and spherical liposomes. The invited authors present the latest results in this exciting multidisciplinary field of their own research group.Many of the contributors working in both fields over many decades were in close collaboration with the late Prof. H. Ti Tien, the founding editor of this book series. There are also chapters written by some of the younger generation of scientists included in this series. This volume keeps in mind the broader goal with both systems, planar lipid bilayers and spherical liposomes, which is thefurther development of this interdisciplinary field worldwide. * Contributions from newcomers and established and experienced researchers* Exploring theoretically and experimentally the planar lipid bilayer systems and spherical liposomes* This volume is dedicated to mark the Bilayer Lipid Membranes 45th anniversary
Download or read book Computational and Theoretical Study of Water and Lipid Dynamics in Biomolecular Systems written by Jhuma Das and published by . This book was released on 2010 with total page 93 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Ph.D. thesis describes three research projects in theoretical and computational biophysics aimed at studying the dynamics of water and lipid molecules in two distinct biomolecular systems. In the first project the energetics and dynamics of water transport through the aquaglyceroporin (GlpF) channel protein is studied by a combination of all-atom molecular dynamics (MD) simulations (both equilibrium and non-equilibrium MD) and stochastic modeling. The MD results are used to determine the potential of mean force and the diffusion coefficient of water molecules crossing the channel. Then, the latter quantities are used to estimate the intrinsic water flux through GlpF, and the corresponding channel permeability. In the second project, by employing a 0.1 micro second long, all-atom MD simulation, the self and correlated dynamics of lipid atoms and molecules in a fully hydrated DMPC lipid bilayer is investigated. The MD simulation results are used to develop a memory function based approach for accurately calculating the lateral self-diffusion coefficient of lipids. In some cases, the proposed memory function method provides a better approach than the currently used ones for determining the lateral diffusion coefficient of lipids in lipid bilayers from the dynamic structure factor measured in inelastic neutron scattering experiments. The purpose of the third project is to investigate the dynamics of water molecules in a hydrated lipid membrane. Using the same MD simulation as in the second project, the anomalous properties of buried and hydration waters (located at the proximity of the fluctuating surface of the lipid membrane) are revealed and contrasted to the properties of bulk water.
