Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Origin of subdiffusion of water molecules on cell membrane surfaces.

ABSTRACT: Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using all-atom molecular dynamics simulations, we show that translational and rotational diffusion of water molecules on lipid membrane surfaces exhibit subdiffusion and aging. Moreover, we provide evidence that both divergent mean trapping time (continuous-time random walk) and long-correlated noise (fractional Brownian motion) contribute to this subdiffusion. These results suggest that subdiffusion on cell membranes causes the water retardation, an enhancement of cell membrane stability, and a higher reaction efficiency.

SUBMITTER: Yamamoto E

PROVIDER: S-EPMC5380161 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Origin of subdiffusion of water molecules on cell membrane surfaces.

Yamamoto Eiji E Akimoto Takuma T Yasui Masato M Yasuoka Kenji K

Scientific reports 20140417

Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using all-atom molecular dynamics simulations, we show that translational and rotational diffusion of water molecules on lipid membrane surfaces exhibit subdiffusion and aging. Moreover, we provide evidence that both divergent mean trapping time (continuous-time random ...[more]

PMID: 24739933

Similar Datasets

Subdiffusion in Membrane Permeation of Small Molecules.

Project description:Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.

| S-EPMC5090971 | biostudies-literature

Resolving mixed mechanisms of protein subdiffusion at the T cell plasma membrane.

Project description:The plasma membrane is a complex medium where transmembrane proteins diffuse and interact to facilitate cell function. Membrane protein mobility is affected by multiple mechanisms, including crowding, trapping, medium elasticity and structure, thus limiting our ability to distinguish them in intact cells. Here we characterize the mobility and organization of a short transmembrane protein at the plasma membrane of live T cells, using single particle tracking and photoactivated-localization microscopy. Protein mobility is highly heterogeneous, subdiffusive and ergodic-like. Using mobility characteristics, we segment individual trajectories into subpopulations with distinct Gaussian step-size distributions. Particles of low-to-medium mobility consist of clusters, diffusing in a viscoelastic and fractal-like medium and are enriched at the centre of the cell footprint. Particles of high mobility undergo weak confinement and are more evenly distributed. This study presents a methodological approach to resolve simultaneous mixed subdiffusion mechanisms acting on polydispersed samples and complex media such as cell membranes.

| S-EPMC5481838 | biostudies-literature

A study of the subdiffusion of small molecules in charged polyelectrolyte multilayers.

Project description:A theoretical approach has been developed here to describe the slow diffusion of small charged molecules of sodium dithionite (S2O42-) in polyelectrolyte multilayers (PEMs) composed of polyallylamine hydrochloride (PAH) and polystyrene sulfonate (PSS), which is demonstrated here to be a case of subdifussion. Diffusion is measured experimentally by recording the quenching of the fluorescence of (7-nitrobenz-2-oxa-1,3-diazol-4yl) amino (NBD) labelled PAH layers assembled on silica particles by flow cytometry. NBD is reduced when it encounters dithionite leading to the disappearance of the fluorescence. The fluorescence decay curves show a slow diffusion of dithionite, that does not follow classical Fickean law. Dithionite diffusion in the PEMs is shown to be a non-Markovian process and the slow diffusion can be described via diffusion equations with fractional time derivatives. Results are explained assuming subdifussion of dithionite in the PEMs, as a result of the trapping of the negatively charged dithionite in the positively charged layers of PAH.

| S-EPMC8604972 | biostudies-literature

Origin of proton affinity to membrane/water interfaces.

Project description:Proton diffusion along biological membranes is vitally important for cellular energetics. Here we extended previous time-resolved fluorescence measurements to study the time and temperature dependence of surface proton transport. We determined the Gibbs activation energy barrier ?G ‡r that opposes proton surface-to-bulk release from Arrhenius plots of (i) protons' surface diffusion constant and (ii) the rate coefficient for proton surface-to-bulk release. The large size of ?G ‡r disproves that quasi-equilibrium exists in our experiments between protons in the near-membrane layers and in the aqueous bulk. Instead, non-equilibrium kinetics describes the proton travel between the site of its photo-release and its arrival at a distant membrane patch at different temperatures. ?G ‡r contains only a minor enthalpic contribution that roughly corresponds to the breakage of a single hydrogen bond. Thus, our experiments reveal an entropic trap that ensures channeling of highly mobile protons along the membrane interface in the absence of potent acceptors.

| S-EPMC5495794 | biostudies-literature

Origin of 1/f noise in hydration dynamics on lipid membrane surfaces.

Project description:Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes.

| S-EPMC4351557 | biostudies-literature

Saturation of charge-induced water alignment at model membrane surfaces.

Project description:The electrical charge of biological membranes and thus the resulting alignment of water molecules in response to this charge are important factors affecting membrane rigidity, transport, and reactivity. We tune the surface charge density by varying lipid composition and investigate the charge-induced alignment of water molecules using surface-specific vibrational spectroscopy and molecular dynamics simulations. At low charge densities, the alignment of water increases proportionally to the charge. However, already at moderate, physiologically relevant charge densities, water alignment starts to saturate despite the increase in the nominal surface charge. The saturation occurs in both the Stern layer, directly at the surface, and in the diffuse layer, yet for distinctly different reasons. Our results show that the soft nature of the lipid interface allows for a marked reduction of the surface potential at high surface charge density via both interfacial molecular rearrangement and permeation of monovalent ions into the interface.

| S-EPMC5903901 | biostudies-other

Specific ions modulate diffusion dynamics of hydration water on lipid membrane surfaces.

Project description:Effects of specific ions on the local translational diffusion of water near large hydrophilic lipid vesicle surfaces were measured by Overhauser dynamic nuclear polarization (ODNP). ODNP relies on an unpaired electron spin-containing probe located at molecular or surface sites to report on the dynamics of water protons within ~10 Å from the spin probe, which give rise to spectral densities for electron-proton cross-relaxation processes in the 10 GHz regime. This pushes nuclear magnetic resonance relaxometry to more than an order of magnitude higher frequencies than conventionally feasible, permitting the measurement of water moving with picosecond to subnanosecond correlation times. Diffusion of water within ~10 Å of, i.e., up to ~3 water layers around the spin probes located on hydrophilic lipid vesicle surfaces is ~5 times retarded compared to the bulk water translational diffusion. This directly reflects on the activation barrier for surface water diffusion, i.e., how tightly water is bound to the hydrophilic surface and surrounding waters. We find this value to be modulated by the presence of specific ions in solution, with its order following the known Hofmeister series. While a molecular description of how ions affect the hydration structure at the hydrophilic surface remains to be answered, the finding that Hofmeister ions directly modulate the surface water diffusivity implies that the strength of the hydrogen bond network of surface hydration water is directly modulated on hydrophilic surfaces.

| S-EPMC3985948 | biostudies-literature

Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds.

Project description:Water molecules at interfaces of materials exhibit enigmatic properties. A variety of spectroscopic studies have observed a high-frequency motion in these water molecules, represented by a blueshift, at both hydrophobic and hydrophilic interfaces. However, the molecular mechanism behind this blueshift has remained unclear. Using Raman spectroscopy and ab initio molecular dynamics simulations, we reveal the molecular mechanism of the blueshift of water molecules around six monosaccharide isomers. In the first hydration shell, we found weak hydrogen-bonded water molecules that cannot have a stable tetrahedral water network. In the water molecules, the vibrational state of the OH bond oriented toward the bulk solvent strongly contributes to the observed blueshift. Our work suggests that the blueshift in various solutions originates from the vibrational motions of these observed water molecules.

| S-EPMC5741398 | biostudies-literature

Persisting water droplets on water surfaces.

Project description:Droplets of various liquids may float on the respective surfaces for extended periods of time prior to coalescence. We explored the features of delayed coalescence in highly purified water. Droplets several millimeters in diameter were released from a nozzle onto a water surface. Results showed that droplets had float times up to hundreds of milliseconds. When the droplets did coalesce, they did so in stepwise fashion, with periods of quiescence interspersed between periods of coalescence. Up to six steps were noted before the droplet finally vanished. Droplets were released in a series, which allowed the detection of unexpected abrupt float-time changes throughout the duration of the series. Factors such as electrostatic charge, droplet size, and sideways motion had considerable effect on droplet lifetime, as did reduction of pressure, which also diminished the number of steps needed for coalescence. On the basis of present observations and recent reports, a possible mechanism for noncoalescence is considered.

| S-EPMC3208511 | biostudies-literature

High-yield activation of scaffold polymer surfaces to attach cell adhesion molecules.

Project description:Zirconium tetra(tert-butoxide) reacts with surface amide groups of polyamide nylon 6/6 to give (eta(2)-amidate)zirconium complexes in high yield. These surface complexes react to bond the cell-adhesive peptide arginine-glycine-aspartic acid (RGD) to the polymer surface. A surface loading of 0.18 nmol/cm(2) of RGD is achieved, which is 20-1000 times higher than previously reported attainable on natural or synthetic polymers by other strategies. Approximately 40% of the nylon surface is covered by the RGD, which gives a surface that is both stable to hydrolysis and highly active for cell adhesion and spreading in vitro.

| S-EPMC2569827 | biostudies-literature

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