Browse
Submit Data
Databases
API
Help

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Kinetics of domain registration in multicomponent lipid bilayer membranes.

ABSTRACT: The kinetics of registration of lipid domains in the apposing leaflets of symmetric bilayer membranes is investigated via systematic dissipative particle dynamics simulations. The decay of the distance between the centres of mass of the domains in the apposing leaflets is almost linear during early stages, and then becomes exponential during late times. The time scales of both linear and exponential decays are found to increase with decreasing strength of interleaflet coupling. The ratio between the time scales of the exponential and linear regimes decreases with increasing domain size, implying that the decay of the distance between the domains' centres of mass is essentially linear for large domains. These numerical results are largely in agreement with the recent theoretical predictions of Han and Haataja [Soft Matter, 2013, 9, 2120-2124]. We also found that the domains become elongated during the registration process.

SUBMITTER: Sornbundit K

PROVIDER: S-EPMC4727538 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Kinetics of domain registration in multicomponent lipid bilayer membranes.

Sornbundit Kan K Modchang Charin C Triampo Wannapong W Triampo Darapond D Nuttavut Narin N Sunil Kumar P B PB Laradji Mohamed M

Soft matter 20141001 37

The kinetics of registration of lipid domains in the apposing leaflets of symmetric bilayer membranes is investigated via systematic dissipative particle dynamics simulations. The decay of the distance between the centres of mass of the domains in the apposing leaflets is almost linear during early stages, and then becomes exponential during late times. The time scales of both linear and exponential decays are found to increase with decreasing strength of interleaflet coupling. The ratio between ...[more]

PMID: 25090030

Similar Datasets

Supramolecular chemistry in lipid bilayer membranes.

Project description:Lipid bilayer membranes form compartments requisite for life. Interfacing supramolecular systems, including receptors, catalysts, signal transducers and ion transporters, enables the function of the membrane to be controlled in artificial and living cellular compartments. In this perspective, we take stock of the current state of the art of this rapidly expanding field, and discuss prospects for the future in both fundamental science and applications in biology and medicine.

| S-EPMC8409493 | biostudies-literature

Gangliosides Destabilize Lipid Phase Separation in Multicomponent Membranes.

Project description:Gangliosides (GMs) form an important class of lipids found in the outer leaflet of the plasma membrane. Typically, they colocalize with cholesterol and sphingomyelin in ordered membrane domains. However, detailed understanding of the lateral organization of GM-rich membranes is still lacking. To gain molecular insight, we performed molecular dynamics simulations of GMs in model membranes composed of coexisting liquid-ordered and liquid-disordered domains. We found that GMs indeed have a preference to partition into the ordered domains. At higher concentrations (>10 mol %), we observed a destabilizing effect of GMs on the phase coexistence. Further simulations with modified GMs show that the structure of the GM headgroup affects the phase separation, whereas the nature of the tail determines the preferential location. Together, our findings provide a molecular basis to understand the lateral organization of GM-rich membranes.

| S-EPMC6818149 | biostudies-literature

Thermodynamics of interleaflet cavitation in lipid bilayer membranes.

Project description:Interleaflet cavitation in lipid bilayer membranes, or, shortly, intramembrane cavitation (IMC), is the formation of gas bubbles between the two leaflets of the membrane. The present paper focuses on the thermodynamics of IMC, namely, on the minimum work required to form an intramembrane cavity. The minimum work can be separated into two parts, one that depends on the volume and number of gas molecules in the bubble and another that depends on the bubble geometry. Minimization of the second part at a fixed bubble volume determines the optimized bubble shape. In homogeneous cavitation this part is proportional to the bubble surface area and therefore the bubble is spherical. In contrast, in IMC the second part is no longer a simple function of the bubble area and the optimized cavity is not spherical because of the finite elasticity of the membrane. Using a simplified assumption about the cavity shape, the geometry-dependent term is derived and minimized at a fixed cavity volume. It is found that the optimized cavity is almost spherical at large bubble volumes, while at small volumes the cavity has a lenslike shape. The optimized shape is used to analyze the minimum work of IMC.

| S-EPMC3620700 | biostudies-literature

Cytoskeletal pinning controls phase separation in multicomponent lipid membranes.

Project description:We study the effect of a minimal cytoskeletal network formed on the surface of giant unilamellar vesicles by the prokaryotic tubulin homolog, FtsZ, on phase separation in freestanding lipid membranes. FtsZ has been modified to interact with the membrane through a membrane targeting sequence from the prokaryotic protein MinD. FtsZ with the attached membrane targeting sequence efficiently forms a highly interconnected network on membranes with a concentration-dependent mesh size, much similar to the eukaryotic cytoskeletal network underlying the plasma membrane. Using giant unilamellar vesicles formed from a quaternary lipid mixture, we demonstrate that the artificial membrane-associated cytoskeleton, on the one hand, suppresses large-scale phase separation below the phase transition temperature, and, on the other hand, preserves phase separation above the transition temperature. Our experimental observations support the ideas put forward in our previous simulation study: In particular, the picket fence effect on phase separation may explain why micrometer-scale membrane domains are observed in isolated, cytoskeleton-free giant plasma membrane vesicles, but not in intact cell membranes. The experimentally observed suppression of large-scale phase separation much below the transition temperatures also serves as an argument in favor of the cryoprotective role of the cytoskeleton.

| S-EPMC4375424 | biostudies-literature

Quantitative visualization of passive transport across bilayer lipid membranes.

Project description:The ability to predict and interpret membrane permeation coefficients is of critical importance, particularly because passive transport is crucial for the effective delivery of many pharmaceutical agents to intracellular targets. We present a method for the quantitative measurement of the permeation coefficients of protonophores by using laser confocal scanning microscopy coupled to microelectrochemistry, which is amenable to precise modeling with the finite element method. The technique delivers well defined and high mass transport rates and allows rapid visualization of the entire pH distribution on both the cis and trans side of model bilayer lipid membranes (BLMs). A homologous series of carboxylic acids was investigated as probe molecules for BLMs composed of soybean phosphatidylcholine. Significantly, the permeation coefficient decreased with acyl tail length contrary to previous work and to Overton's rule. The reasons for this difference are considered, and we suggest that the applicability of Overton's rule requires re-evaluation.

| S-EPMC2567174 | biostudies-literature

Construction of P-glycoprotein incorporated tethered lipid bilayer membranes.

Project description:To investigate drug-membrane protein interactions, an artificial tethered lipid bilayer system was constructed for the functional integration of membrane proteins with large extra-membrane domains such as multi-drug resistance protein 1 (MDR1). In this study, a modified lipid (i.e., 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino (polyethylene glycol)-2000] (DSPE-PEG)) was utilized as a spacer molecule to elevate lipid membrane from the sensor surface and generate a reservoir underneath. Concentration of DSPE-PEG molecule significantly affected the liposome binding/spreading and lipid bilayer formation, and 0.03 mg/mL of DSPE-PEG provided optimum conditions for membrane protein integration. Further, the incorporation of MDR1 increased the local rigidity on the platform. Antibody binding studies showed the functional integration of MDR1 protein into lipid bilayer platform. The platform allowed to follow MDR!-statin-based drug interactions in vitro. Each binding event and lipid bilayer formation was monitored in real-time using Surface Plasmon Resonance and Quartz Crystal Microbalance-Dissipation systems, and Atomic Force Microscopy was used for visualization experiments.

| S-EPMC5668657 | biostudies-literature

The aliphatic chain of cholesterol modulates bilayer interleaflet coupling and domain registration.

Project description:Cholesterol is a necessary component and critical regulator of liquid-ordered membrane domains. However, the structural features that determine its unique physicochemical behaviors are not fully understood. In particular, very little is known about the specific functions of the terminal aliphatic chain of cholesterol, as previous studies have focused mainly on the rigid sterol ring structure and its hydroxyl head. In the current work, we used coarse-grained molecular dynamics simulations to investigate the effect of cholesterol aliphatic chain length on the dynamics and structure of coexisting lipid domains. We found that the aliphatic chain has no appreciable effect on phase separation per se, but it significantly affects the rate of cholesterol flip-flop and intermonolayer interaction. These effects are accompanied by changes in domain dynamics, lateral pressure, and interleaflet coupling. Our study provides useful insight into how biological sterols modulate communication between the outer and inner surfaces of the plasma membrane and, therefore, cellular signaling.

| S-EPMC5064870 | biostudies-literature

Oligomeric structure of colicin ia channel in lipid bilayer membranes.

Project description:Colicin Ia is a soluble, harpoon-shaped bacteriocin which translocates across the periplasmic space of sensitive Escherichia coli cell by parasitizing an outer membrane receptor and forms voltage-gated ion channels in the inner membrane. This process leads to cell death, which has been thought to be caused by a single colicin Ia molecule. To directly visualize the three-dimensional structure of the channel, we generated two-dimensional crystals of colicin Ia inserted in lipid-bilayer membranes and determined a approximately 17 three-dimensional model by electron crystallography. Supported by velocity sedimentation, chemical cross-linking and single-particle image analysis, the three-dimensional structure is a crown-shaped oligomer enclosing a approximately 35 A-wide extrabilayer vestibule. Our study suggests that lipid insertion instigates a global conformational change in colicin Ia and that more than one molecule participates in the channel architecture with the vestibule, possibly facilitating the known large scale peptide translocation upon channel opening.

| S-EPMC2713560 | biostudies-literature

Computation of Forster Resonance Energy Transfer in Lipid Bilayer Membranes.

Project description:Calculations of Förster Resonance Energy Transfer (FRET) often neglect the influence of different chromophore orientations or changes in the spectral overlap. In this work, we present two computational approaches to estimate the energy transfer rate between chromophores embedded in lipid bilayer membranes. In the first approach, we assess the transition dipole moments and the spectral overlap by means of quantum chemical calculations in implicit solvation, and we investigate the alignment and distance between the chromophores in classical molecular dynamics simulations. In the second, all properties are evaluated integrally with hybrid quantum mechanical/molecular mechanics (QM/MM) calculations. Both approaches come with advantages and drawbacks, and despite the fact that they do not agree quantitatively, they provide complementary insights on the different factors that influence the FRET rate. We hope that these models can be used as a basis to optimize energy transfers in nonisotropic media.

| S-EPMC9639162 | biostudies-literature

Lipid Interactions and Organization in Complex Bilayer Membranes.

Project description:Bilayer lipids influence the lateral structure of the membranes, but the relationship between lipid properties and the lateral structure formed is not always understood. Model membrane studies on bilayers containing cholesterol and various phospholipids (PLs) suggest that high and low temperature melting PLs may segregate, especially in the presence of cholesterol. The effect of different PL headgroups on lateral structure of bilayers is also not clear. Here, we have examined the formation of lateral heterogeneity in increasingly complex (up to five-component) multilamellar bilayers. We have used time-resolved fluorescence spectroscopy with domain-selective fluorescent probes (PL-conjugated trans-parinaric acid), and (2)H NMR spectroscopy with site or perdeuterated PLs. We have measured changes in bilayer order using such domain-selective probes both as a function of temperature and composition. Our results from time-resolved fluorescence and (2)H NMR showed that in ternary bilayers, acyl chain order and thermostability in sphingomyelin-rich domains were not affected to any greater extent by the headgroup structure of the monounsaturated PLs (phosphatidylcholine, phosphatidylethanolamine, or phosphatidylserine) in the bilayer. In the complex five-component bilayers, we could not detect major differences between the different monounsaturated PLs regarding cholesterol-induced ordering. However, cholesterol clearly influenced deuterated N-palmitoyl sphingomyelin differently than the other deuterated PLs, suggesting that cholesterol favored N-palmitoyl sphingomyelin over the other PLs. Taken together, both the fluorescence spectroscopy and (2)H NMR data suggest that the complex five-component membranes displayed lateral heterogeneity, at least in the lower temperature regimen examined.

| S-EPMC4833832 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data