Lipids and lipid bilayers

Properties of Lipids and Lipid Bilayers Lipid bilayers formed between two aqueous phases have this important property they form two-dimensional sheets, the edges of which close upon each other and undergo self-sealing to form liposomes. 

Other biomolecules that are of interest in p.CP are lipids and lipid bilayers. Supported lipid bilayers are very fragile assemblies that are formed by lipids that are organized into two opposing leaflets on hydrophilic surfaces, such as glass or mica substrates. These structures can be also patterned on solid substrates but the p.CP technique differs slightly from the ones that were applied for proteins or DNA. First, the bilayer has to be formed on the oxidized PDMS stamp from the buffer solution by lipid vesicle fusion. Second, printing has to be carried out in water, otherwise the bilayer will lose its structure.99 This method allows efficient and reliable transfer of membrane patches to glass surfaces. 

Lyubartsev, A. P. (2005). Multiscale modeling of lipids and lipid bilayers. European Biophysics Journal, 35, 53. 

Protems can be physisorbed or covalently attached to mica. Another method is to innnobilise and orient them by specific binding to receptor-fiinctionalized planar lipid bilayers supported on the mica sheets [15]. These surfaces are then brought into contact in an aqueous electrolyte solution, while the pH and the ionic strength are varied. Corresponding variations in the force-versus-distance curve allow conclusions about protein confomiation and interaction to be drawn [99]. The local electrostatic potential of protein-covered surfaces can hence be detemiined with an accuracy of 5 mV. 

The adliesion and fiision mechanisms between bilayers have also been studied with the SEA [M, 100]. Kuhl et al [17] found that solutions of short-chained polymers (PEG) could produce a short-range depletion attraction between lipid bilayers, which clearly depends on the polymer concentration (fignre Bl.20.1 It. This depletion attraction was found to mduce a membrane fusion widiin 10 minutes that was observed, in real-time, using PECO fringes. There has been considerable progress in the preparation of fluid membranes to mimic natural conditions in the SEA [ ], which promises even more exciting discoveries in biologically relevant areas. 

Flelfrioh W 1973 Elastio properties of lipid bilayers theory and possible experiments Z. Naturf. c 28 693... 

Niu S and Mauzerall D 1996 Fast and efficient charge transport across a lipid bilayer is electronically mediated by Cyf, fullerene aggregates J. Am. Chem. Soc. 118 5791-5... 

Hwang K C and Mauzerall D C 1993 Photoinduced electron transport across a lipid bilayer mediated by Nature 361 138-40... 

Hwang K C and Mauzerall D C 1992 Vectorial electron transfer from an interfacial photoexcited porphyrin to ground-state Cgg and C g and from ascorbate to triplet Cgg and C g in a lipid bilayer J. Am. Chem. Soc. 114 9705-6... 

Schwarz G 1996 Peptides at lipid bilayers and at the air/water interface Ber. Bunsenges. Rhys. Chem. 100 999-1003... 

In special cases (as in colloidal solutions) some particles can be considered as essential and other particles as irrelevant , but in most cases the essential space will itself consist of collective degrees of freedom. A reaction coordinate for a chemical reaction is an example where not a particle, but some function of the distance between atoms is considered. In a simulation of the permeability of a lipid bilayer membrane for water [132] the reaction coordinate was taken as the distance, in the direction perpendicular to the bilayer, between the center of mass of a water molecule and the center of mass of the rest of the system. In proteins (see below) a few collective degrees of freedom involving all atoms of the molecule, describe almost all the... 

There has been considerable interest in the simulation of lipid bilayers due to their biological importance. Early calculations on amphiphilic assemblies were limited by the computing power available, and so relatively simple models were employed. One of the most important of these is the mean field approach of Marcelja [Marcelja 1973, 1974], in which the interaction of a single hydrocarbon chain with its neighbours is represented by two additional contributions to the energy function. The energy of a chain in the mean field is given by ... 

The summation runs over all carbon atoms in the chain. is the angle between the bilayei normal and the molecular axis, as discussed above. is the field strength this may be parametrised to reproduce appropriate experimental data such as the deuterium NMR order parameters or it may be obtained by a self-consistent protocol, as described below. In his work on lipid bilayers Marcelja used a slightly different expression for i jjisp which... 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

Phosphatidylcholine is an important component of cell membranes but cell mem branes are more than simply lipid bilayers Although their composition varies with their source a typical membrane contains about equal amounts of lipid and protein and the amount of cholesterol m the lipid fraction can approximate that of phosphatidylcholine The lipid fraction is responsible for the structure of the membrane Phosphatidyl choline provides the bilayer that is the barrier between what is inside the cell and what IS outside Cholesterol intermingles with the phosphatidylcholine to confer an extra measure of rigidity to the membrane... 

Section 26 4 Phospholipids are intermediates in the biosynthesis of triacylglycerols from fatty acids and are the principal constituents of the lipid bilayer component of cell membranes... 

Lipid bilayer (Section 26 4) Arrangement of two layers of phospholipids that constitutes cell membranes The polar termini are located at the inner and outer membrane-water interfaces and the lipophilic hydrocarbon tails cluster on the inside... 

Biological membranes provide the essential barrier between cells and the organelles of which cells are composed. Cellular membranes are complicated extensive biomolecular sheetlike structures, mostly fonned by lipid molecules held together by cooperative nonco-valent interactions. A membrane is not a static structure, but rather a complex dynamical two-dimensional liquid crystalline fluid mosaic of oriented proteins and lipids. A number of experimental approaches can be used to investigate and characterize biological membranes. However, the complexity of membranes is such that experimental data remain very difficult to interpret at the microscopic level. In recent years, computational studies of membranes based on detailed atomic models, as summarized in Chapter 21, have greatly increased the ability to interpret experimental data, yielding a much-improved picture of the structure and dynamics of lipid bilayers and the relationship of those properties to membrane function [21]. 

Specification of. S SkCG, CO) requires models for the diffusive motions. Neutron scattering experiments on lipid bilayers and other disordered, condensed phase systems are often interpreted in terms of diffusive motions that give rise to an elastic line with a Q-dependent amplitude and a series of Lorentzian quasielastic lines with Q-dependent amplitudes and widths, i.e.. 

Figure 13 Center-of-mass mean-square displacements computed from MD simulations at 323 K. (a) DPPC motion in the plane of a lipid bilayer averaged over 10 ps (b) DPPC motion in the plane of a lipid bilayer averaged over 100 ps (c) comparison of the DPPC m-plane mean-square displacement to linear and power law functions of time (d) comparison of the center-of-mass mean-square displacement from an MD simulation of liquid tetradecane to a linear function of time.

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 

In contrast, the transmembrane helices observed in the reaction center are embedded in a hydrophobic surrounding and are built up from continuous regions of predominantly hydrophobic amino acids. To span the lipid bilayer, a minimum of about 20 amino acids are required. In the photosynthetic reaction center these a helices each comprise about 25 to 30 residues, some of which extend outside the hydrophobic part of the membrane. From the amino acid sequences of the polypeptide chains, the regions that comprise the transmembrane helices can be predicted with reasonable confidence. 

Alphaviruses, such as Sindbis virus and Semliki Forest virus, are a group of mosquito-borne, enveloped RNA viruses that can cause encephalitis, fever, arthritis and rashes in mammals. These viruses have two protein shells—an outer glycoprotein layer and an inner core— which are separated by a lipid bilayer, a membrane. Studies by cryoelectron microscopy have shown that... 

Whereas the main challenge for the first bilayer simulations has been to obtain stable bilayers with properties (e.g., densities) which compare well with experiments, more and more complex problems can be tackled nowadays. For example, lipid bilayers were set up and compared in different phases (the fluid, the gel, the ripple phase) [67,68,76,81]. The formation of large pores and the structure of water in these water channels have been studied [80,81], and the forces acting on lipids which are pulled out of a membrane have been measured [82]. The bilayer systems themselves are also becoming more complex. Bilayers made of complicated amphiphiles such as unsaturated lipids have been considered [83,84]. The effect of adding cholesterol has been investigated [85,86]. An increasing number of studies are concerned with the important complex of hpid/protein interactions [87-89] and, in particular, with the structure of ion channels [90-92]. 

Baumgartner and coworkers [145,146] study lipid-protein interactions in lipid bilayers. The lipids are modeled as chains of hard spheres with heads tethered to two virtual surfaces, representing the two sides of the bilayer. Within this model, Baumgartner [145] has investigated the influence of membrane curvature on the conformations of a long embedded chain (a protein ). He predicts that the protein spontaneously localizes on the inner side of the membrane, due to the larger fluctuations of lipid density there. Sintes and Baumgartner [146] have calculated the lipid-mediated interactions between cylindrical inclusions ( proteins ). Apart from the... 

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