Fast two dimensional computer simulation of bilayer hemifusion

Computer simulation of model membranes was used to evaluate the possible mechanism of lipid bilayer fusion. The simplified two dimensional model of the membrane cross section was used as an analog of three dimensional reality. Lipid molecules were represented by rod-like structures, and forces between them were limited to attraction/repulsion interactions described by a simple energy function with a minimum; 300-400 molecules were modeled in every simulation. Using the energy minimization procedure, it was possible to obtain stable linear or circular bilayer structures (two dimensional analogs of planar membranes and liposomes). In response to changes in attraction/repulsion equilibrium between molecules these bilayers were able to reorganize via cooperative process. By increasing the headgroup attraction parameter for contacting monolayers, it was possible to induce formation of a zone of hemifusion in the area of bilayer contact. The possible correlation between cooperative bilayer rearrangement in the model and in real bilayers is discussed.     

Temperature dependence of polypeptide partitioning between water and phospholipid bilayers

Various thermodynamic forces (e.g., the hydrophobic effect, electrostatic interactions, peptide immobilization, peptide conformational changes, "bilayer effects," and van der Waals dispersion forces) can participate in the transfer of polypeptides from aqueous solution into lipid bilayers. To investigate the contributions of these forces to peptide-membrane thermodynamics, we have studied the temperature dependence of the water-bilayer partitioning of 4 polypeptides derived from the first 25 amino acid residues in the presequence of subunit IV of yeast cytochrome c oxidase (Cox IVp) using electron paramagnetic resonance spectroscopy. The partitioning of the Cox IVp peptides into phospholipid bilayers increases as the temperature is increased from 3 to 40 degrees C. The contribution of bilayer surface expansion to the temperature-dependent partitioning is estimated to be relatively small and to contribute minimally to the increased bilayer binding of the peptides with increasing temperature. Thermodynamic analysis of the data shows that the transfer of the peptides from water into bilayers at 298 K is driven by the entropic term (-T delta Str) with values ranging from -6.7 to -10 kcal mol-1, opposed by the enthalpic term (delta Htr) by approximately 4 kcal mol-1, and accompanied by a change in heat capacity (delta Cp) ranging from -117 to -208 cal K-1 mol-1. Our results indicate that while a variety of forces do, in fact, contribute to the transfer free energies (delta Gtr), the major driving force for the water-to-bilayer transfer is the hydrophobic effect.     

The adhesion strength of the composition coating with a polymer matrix based on sodium carboxymethylcellulose with a metallic filler made from aluminum powder

In order to interpret the adhesion regularities, a way to make coagulants from fine fractions of aluminum powder on the microroughness of steel surface, providing the adhesion strength of coating due to the van der Waals interaction forces, is suggested. The role of the plasticizer as a factor increasing the adhesion strength of coatings via decreasing the internal stresses in the composition material and at the interface between the steel surface and coating is established.     

Methodological issues in conducting a survey of construction workers in northeastern Thailand

We have studied the effects of D-threo-1-phenyl-2-decanoylamino-3-morpholino-1-propanol (D-PDMP) and its L-enantiomer on glycosphingolipids in cultured normal human kidney proximal tubular cells. We found that D-PDMP exerted a concentration-dependent reduction in the metabolic labelling and cellular levels of glucosylceramide (GlcCer), lactosylceramide (LacCer), and the globo-series glycosphingolipids, GbOSe3Cer and GbOse4Cer. It also directly inhibited the activity of UDP-glucose:ceramide beta 1--> 4-glucosyltransferase (GlcT-1) and UDP-galactose: GlcCer beta 1-->4 galactosyltransferase (GalT-2). In contrast, L-PDMP had opposite effects on the metabolic labelling of GlcCer, LacCer, and GbOse3Cer. The levels of GlcCer and LacCer were increased, while the labelling and level of GbOse4Cer were strongly reduced. Purified GalT-2 from human kidney was inhibited by D-PDMP and stimulated by L-PDMP. It appears likely that the different glycosphingolipid glycosyltransferases possess similar binding sites for the ceramide moiety, which are blocked by binding to D-PDMP and, in the case of GbOse4Cer synthase, by L-PDMP as well. The stimulatory effects of L-PDMP on GlcCer and LacCer synthases may be the result of binding to a modulatory site on the glycosyltransferases; in intact cells, the enzyme-analog complex may afford protection against the normal catabolic inactivation of the enzymes.     

Globoside as a membrane receptor: a consideration of oligosaccharide communication with the hydrophobic domain

Recognition of macromolecules by glycosphingolipids is closely correlated with the nature of the glycolipid carbohydrate; however, it is also thought to be secondarily modulated by the structure of the single fatty acid. In the present work, we sought insight into what physical effect a change in this fatty acid has on the extramembranous portion of globosides at liposomal surfaces mimicking systems for which modulated receptor function has been recorded in the past. Protons of the exocyclic hydroxymethyl group on the terminal Gal residue of globotriaosylceramide (Gb3) were replaced with deuterium. In this location, the nonperturbing probe nuclei sampled cumulative conformational and orientational characteristics of the oligosaccharide chain at a sugar residue that is critical in specific binding of verotoxins. Deuterated Gb3 having 18:1 fatty acid was compared to the same species having 22:1 fatty acid, at 6.3 mol % in unsonicated bilayers of dipalmitoylphosphatidylcholine/cholesterol. Both produced narrow, apparently axially asymmetric 2H NMR spectra over a wide temperature range. Motional properties of the terminal sugar were measurably influenced by the fluidity of the host matrix; however, evidence was not found for conformational or orientational variation in this sugar brought about by the fatty acid alteration. In related experiments, acetate protons on the terminal N-acetyl galactosamine (GalNAc) residue of globotetraosylceramide (Gb4) were substituted with deuterium, and the natural fatty acid was replaced with 18:0 or 24:0 species deuterated at C2. Once again, species with short vs long fatty acid were examined for evidence of headgroup differences. Spectra of Gb4 were compared at 10 mol % in unsonicated fluid bilayers of 1-palmitoyl-2-oleoylphosphatidylcholine, and at 5 mol % in membranes containing 33 mol% cholesterol. Spectral splittings reflecting cumulative effects on conformation and order at the terminal deuterated sugar remained unchanged between species having 18:0 vs 24:0 fatty acid in POPC/cholesterol. In a pure POPC host matrix, there was clear evidence of a motional difference between the two--the longer chain Gb4 demonstrating spectral asymmetry--but the spectral width was unchanged. Transverse relaxation times, T2, were measured. Our findings appear to help correlate the conclusions of a number of workers dealing with the molecular basis of crypticity. We suggest that changes in glycolipid receptor function based on ceramide fatty acid variation have a major origin in the fatty acid's ability to determine the thermodynamics of interaction with the host matrix, as reflected in such parameters as glycolipid motional properties, local membrane curvature, and likely glycolipid time-dependent lateral associations. The result at low concentrations of glycolipid may often be only a subtly altered collective surface epitope, best detected by a specific recognition event.     

Pulmonary surfactant protein SP-B interacts similarly with dipalmitoylphosphatidylglycerol and dipalmitoylphosphatidylcholine in phosphatidylcholine/phosphatidylglycerol mixtures

Porcine pulmonary surfactant-associated protein SP-B was incorporated into bilayers of chain-perdeuterated dipalmitoylphosphatidylglycerol (DPPG-d62) and into bilayers containing 70 mol % dipalmitoylphosphatidylcholine (DPPC) and 30 mol % DPPG-d62 or 70 mol % chain-perdeuterated DPPC (DPPC-d62) and 30 mol % DPPG. The effect of SP-B on the phase behavior, lipid chain order, and dynamics in these bilayers was examined using deuterium nuclear magnetic resonance (2H-NMR). In both DPPG-d62 and the mixed lipid system, SP-B is found to have little effect on chain order in the liquid crystalline phase. With 11% (w/w) SP-B present, both bilayer systems display a continuous change from liquid crystal to gel with no evidence of two-phase coexistence near the transition. Despite its limited effect on chain order in these bilayers, SP-B is found to strongly perturb chain deuteron transverse relaxation in the liquid crystal and gel phases of DPPG-d62 and the DPPC/DPPG (7:3) mixtures. The observation that SP-B associates with the bilayer in a way which substantially alters the slow motions responsible for transverse relaxation without significantly affecting chain order in either the liquid crystal or gel phases may place some constraints on possible models for that association.     

Developmental changes of neutral glycosphingolipids as receptors for pulmonary surfactant protein SP-A in the alveolar epithelium of murine lung

A dramatic change in the glycosphingolipid composition in murine lung occurred between 1 day and 1 week after birth. GlcCer and LacCer were the predominant neutral glycosphingolipids prenatally and 1 day after birth, and the concentrations of globo- and ganglio-series glycosphingolipids increased abruptly from 1 week after birth, reaching maxima at 2-3 weeks. To explore the functional significance of the change, we examined the role of neutral glycosphingolipids as receptors for the murine pulmonary surfactant protein, SP-A, and found that SP-A bound to LacCer, Gg3Cer, and Gg1Cer, but not to Gb3Cer, Gb4Cer, IV3GalNAc alpha-Gb4Cer, sulfatide, or several gangliosides. On TLC-blotting with 125I-labeled SP-A, the binding of SP-A to Gg3Cer and Gg4Cer was 5 times higher than that to LacCer, and on immunohistochemical staining Gg4Cer and Gg3Cer was mainly observed in the alveolar epithelium. Thus, the capacity to retain SP-A of glycolipid receptors per gram dry weight of lung at 1 week after birth was 1.6 times higher than that at 1 day after birth, and reached a maximum 3 weeks after birth. These findings suggest that the enhanced synthesis of the ganglio-series neutral glycosphingolipids 1 week after birth results in an increase in the binding capacity for SP-A on the epithelial cell surface of alveoli.     

Analysis of membrane protein self-association in lipid systems by fluorescence particle counting: application to the dihydropyridine receptor

Fluorescence particle counting (FPC) is employed to analyze the distribution of a purified membrane protein, the dihydropyridine receptor (DHP-R), in detergent micelles, in lipid vesicles, and in lipid monolayers generated from the vesicles. The method was used to identify conditions for which DHP-Rs occur singly distributed in micelles and in vesicles. In monolayers, the DHP-R showed self-association, starting from monomeric distribution at concentrations (c) of typically 10 DHP-R/microm2. The average cluster size [m(t)] of associates was followed by FPC in time and the dependence of the lateral diffusion constant [D(lat)(m,pi)] of the associates on the surface pressure (pi) was determined. By studying the dependence of m(t) on c, pi, D(lat)(pi), and salt concentration (c(s)), we derived an empirical expression for the association rate constant (k(a)) and for m(t) that fits the experimental m(t) relations. Theoretical justification for these dependencies is obtained from collision theory, leading to a mechanistic picture of the aggregation process. DHP-R association is irreversible. Its rate is not diffusion-limited. A large number of collisions is required to overcome an interaction energy barrier of about 6-11 kT, depending on m and c(s) but not on pi. The increase in association rate with increasing average cluster size m is related to increasing van der Waals attraction, while the increase in rate with increasing c(s) relates to decreasing electrostatic repulsion. Van der Waals and electrostatic forces represent, however, only part of the interaction energy. The main contribution was not dependent on the variables studied and, most likely, reflects hydration forces which need to be overcome for association.     

Hybrid bilayer membranes in air and water: infrared spectroscopy and neutron reflectivity studies

In this report we describe the fabrication and characterization of a phospholipid/alkanethiol hybrid bilayer membrane in air. The bilayer is formed by the interaction of phospholipid with the hydrophobic surface of a self-assembled alkanethiol monolayer on gold. We have characterized the resulting hybrid bilayer membrane in air using atomic force microscopy, spectroscopic ellipsometry, and reflection-absorption infrared spectroscopy. These analyses indicate that the phospholipid added is one monolayer thick, is continuous, and exhibits molecular order which is similar to that observed for phospholipid/phospholipid model membranes. The hybrid bilayer prepared in air has also been re-introduced to water and characterized using neutron reflectivity and impedance spectroscopy. Impedance data indicate that when moved from air to water, hybrid bilayers exhibit a dielectric constant and thickness that is essentially equivalent to hybrid bilayers prepared in situ by adding phospholipid vesicles to alkanethiol monolayers in water. Neutron scattering from these samples was collected out to a wave vector transfer of 0.25 A(-1), and provided a sensitivity to changes in total layer thickness on the order of 1-2 A. The data confirm that the acyl chain region of the phospholipid layer is consistent with that observed for phospholipid-phospholipid bilayers, but suggest greater hydration of the phospholipid headgroups of HBMs than has been reported in studies of lipid multilayers.     

THE INFLUENCE OF VAN DER WAALS FORCE ON THE SINTERING OF GLASS

Abstract

The contribution of van der Waals forces to the sintering of glass particles has been estimated. The contribution appears to be small relative to surface-tension forces in practical cases, but may be of importance in the formation of the initial bond during sintering.     

Closure behaviour of small cracks

Measurements of the initiation, growth, and closure behaviour of micro-cracks are reported for one ferritic and one austenitic low strength steel. Interferometric measurements of the COD of small surface cracks were performed with a resolution of 3 nm in order to measure the closure behaviour of micro-cracks. The van der Waals forces between atoms were added numerically in order to calculate the normal as well as the tangential forces acting between closely separated crack faces. The results are discussed in the context of the growth and closure of micro-cracks.     

Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy

We have used self-assembled purines and pyrimidines on planar gold surfaces and on gold-coated atomic force microscope (AFM) tips to directly probe intermolecular hydrogen bonds. Electron spectroscopy for chemical analysis (ESCA) and thermal programmed desorption (TPD) measurements of the molecular layers suggested monolayer coverage and a desorption energy of about 25 kcal/mol. Experiments were performed under water, with all four DNA bases immobilized on AFM tips and flat surfaces. Directional hydrogen-bonding interaction between the tip molecules and the surface molecules could be measured only when opposite base-pair coatings were used. The directional interactions were inhibited by excess nucleotide base in solution. Nondirectional van der Waals forces were present in all other cases. Forces as low as two interacting base pairs have been measured. With coated AFM tips, surface chemistry-sensitive recognition atomic force microscopy can be performed.     

Mitochondrial presequence inserts differently into membranes containing cardiolipin and phosphatidylglycerol

The interaction of the 25-residue presequence of yeast cytochrome oxidase subunit IV with lipid bilayers composed of phosphatidylglycerol, cardiolipin, or their (1:4) mixtures with phosphatidylcholine has been studied by spin-label ESR spectroscopy. Binding of the presequence progressively broadens the gel-to-fluid phase transition of dimyristoylphosphatidylglycerol bilayers, leading to abolition of the transition at a peptide/lipid ratio of > or = 1:5 mol/mol. The mobility of phosphatidylglycerol spin-labeled at the 5-position of the sn-2 chain is decreased in both gel and fluid phases on binding the presequence, with a progressively increasing ESR spectral anisotropy in the fluid phase. The ESR spectra of phosphatidylglycerol spin-labeled at the 14-position of the sn-2 chain contain a second motionally restricted component, in addition to the fluid bilayer spectral component, that arises from direct interaction of the bound presequence with the lipid chains. The proportion of this motionally restricted component is greater for dioleoylphosphatidylglycerol bilayers (corresponding to 2-3 lipids per peptide) than for cardiolipin bilayers (1-2 lipids/peptide), and this component is present also in the mixed bilayers containing 80% phosphatidylcholine. The ESR spectra of the presequence spin-labeled with a maleimide derivative at cysteine-19 evidence high mobility in solution and a very strong reduction in mobility on binding to bilayers containing negatively charged lipids. At low peptide to lipid ratios, the ESR spectra of the spin-labeled presequence sense the phase transition of dimyristoylphosphatidylglycerol.(ABSTRACT TRUNCATED AT 250 WORDS)     

The folding of centromeric DNA strands into intercalated structures: a physicochemical and computational study

We have carried out a physicochemical and computational analysis on the stability of the intercalated structures formed by cytosine-rich DNA strands. In the computational study, the electrostatic energy components have been calculated using a Poisson-Boltzmann model, and the non-polar energy components have been computed with a van der Waals function and/or a term dependent on the solvent-accessible surface area of the molecules. The results have been compared with those obtained for Watson-Crick duplexes and with thermodynamic data derived from UV experiments. We have found that intercalated DNA is mainly stabilized by very favorable electrostatic interactions between hydrogen-bonded protonated and neutral cytosines, and by non-polar forces including the hydrophobic effect and enhanced van der Waals contacts. Cytosine protonation electrostatically promotes the association of DNA strands into a tetrameric structure. The electrostatic interactions between stacked C.C+ pairs are strongly attenuated by the reaction field of the solvent, and are modulated by a complex interplay of geometric and protonation factors. The forces stabilizing intercalated DNA must offset an entropic penalty due to the uptake of protons for cytosine protonation, at neutral pH, and also the electrostatic contribution to the solvation free energy. The latter energy component is less favorable for protonated DNA due to the partial neutralization of the negative charge of the molecule, and probably affects other protonated DNA and RNA structures such as C+-containing triplexes.     

Structural phase transitions involved in the interaction of phospholipid bilayers with octyl glucoside

The transitional stages induced by the interaction of the nonionic surfactant octyl glucoside (OcOse) on phosphatidylcholine liposomes were studied by means of transmission electron microscopy (TEM), light scattering and permeability changes. A linear correlation was observed between the effective surfactant/lipid molar ratio (Re; three-stage model proposed for liposome solubilization) and the OcOse concentration in the initial and final interaction stages, despite showing almost a constant value during bilayer saturation. The bilayer/aqueous phase partition coefficient (K) decreased in the subsolubilizing interaction steps and increased during solubilization. Thus, whereas a preferential distribution of surfactant monomers in the aqueous phase with respect to the lipid bilayers took place in the initial interaction steps, a larger association of OcOse molecules with these lipids in bilayers occurred during solubilization. The initial steps of bilayer saturation (50-70% permeability) were attained for a lower free surfactant (Sw) than that for its critical micellar concentration (cmc). When Sw reached the OcOse cmc, solubilization started to occur (Resat). Large unilamellar vesicles began to form as the OcOse exceeded 60 mol/100 mol, exhibiting for 65 mol/100 mol (50% permeability) vesicles of approximately 400 nm. TEM pictures for 100% permeability (72 mol/100 mol) and Resat still showed unilamellar vesicles, albeit that the Resat TEM picture showing traces of smaller structures. Exceeding surfactant amounts led to a decrease in static light scattering; the vesicle-size curve began to show a bimodal distribution. The TEM picture showed tubular structures together with bilayer fragments. Thereafter, the open structures were gradually affected by the surfactant and the scattered intensity gradually decreased to a constant low value.     

Local interactions as a structure determinant for protein molecules: III

Investigation of the known protein structures has led to the generalization that the native folding permits each sidechain to select those nearest-neighbors which maximize stabilization from van der Waals interactions. With regard to secondary structure: 1. Helical and beta regions exhibit characteristic patterns of short-range contacts (residue numbers k and k + t with [t] less than or equal to 4) due to the geometries of these secondary structures. However, these are not strictly obligatory, and preferred short-range contacts which would result in unfavorable van der Waals interactions are replaced by favorable long-range contacts. 2. The generalization mentioned at the outset holds for individual proteins, both for short-range and long-range contacts, and without regard for the type or amount of secondary structure present. 3. These observations imply that van der Waals interactions arising from short-range contacts partially determine secondary structure, and this is demonstrated by tests based upon assignment of regions of secondary structure in the known proteins. The principle of optimizing van der Waals stabilization from long-range contacts is applied to predict the structure of the complex formed by the S-peptide and S-protein of ribonuclease-S. The formation of favorable pairs is found to be more important than the total number of intermolecular contacts, and 40 to 50% of this stabilization is contributed by two residues of the S-peptide, Phe-8 and Met-13.     

多孔介质中微观力的作用及渗流模型

在现有微尺度流动实验和理论认识的基础上,建立了包含范德华力、静电力、空间位型力、表面张力等微观力的特性方程,分析了影响多孔介质中流体流动的微观力种类和作用范围.通过建立考虑微观力作用的圆管流动数学模型,构造了考虑微观力作用的多孔介质的毛管束网络数学模型,推导了考虑微观力作用的相对渗透率模型.通过模拟分析阐明了微观力在多孔介质壁面上的作用及对渗流的影响.模拟结果表明微观力在细小孔隙流动中不可忽略.      

Experimental study of the interaction range and association rate of surface-attached cadherin 11

We describe a method allowing quantitative determination of the interaction range and association rate of individual surface-attached molecules. Spherical beads (1.4 micro(m) radius) were coated with recombinant outer domains of the newly described classical type II cadherin 11, a cell adhesion molecule. Beads were driven along cadherin-coated surfaces with a hydrodynamic force of approximately 1 pN, i.e., much less than the mechanical strength of many ligand-receptor bonds. Spheres displayed periods of slow motion interspersed with arrests of various duration. Particle position was monitored with 50 Hz frequency and 0.025 micro(m) accuracy. Nearly 1 million positions were recorded and processed. Comparison between experimental and computer-simulated trajectories suggested that velocity fluctuations might be related quantitatively to Brownian motion perpendicular to the surface. The expected amplitude of this motion was of order of 100 nm. Theoretical analysis of the relationship between sphere acceleration and velocity allowed simultaneous determination of the wall shear rate and van der Waals attraction between spheres and surface. The Hamaker constant was estimated at 2.9 x 10(-23) J. The frequency of bond formation was then determined as a function of sphere velocity. Experimental data were consistent with the view that the rate of association between a pair of adhesion molecules was approximately 1.2 x 10(-3) s-1 and the interaction range was approximately 10 nm. It is concluded that the presented methodology allows sensitive measurement of sphere-to-surface interactions (with approximately 10 fN sensitivity) as well as the effective range and rate of bond formation between individual adhesion molecules.     

Role of Microscopic Physicochemical Forces in Large Volumetric Strains for Clay Sediments

In a clay-water-electrolyte system, each particle is under the influence of van der Waals attraction, electrical double-layer repulsion, Born's repulsion, hydrodynamic viscous drag, and gravity. This study investigates the role of microscopic forces in the volumetric behavior of clay sediments. The microscopic forces are implemented in a 2D discrete element method (DEM) framework that uses spheres to represent clay particles. The model is validated with two well-defined problems: (1) an analytical estimation of force-equilibrium for the system of colloidal particles; and (2) the theoretical settling velocity of spherical particles according to Stokes' law. An experimental program is developed to measure the free swell of Georgia kaolinite, Na-montmorillonite, and Ca-montmorillonite. The experimental results are used to validate the DEM framework in its ability to correctly model the volumetric strains inherent to clay sediments. A good agreement between the model prediction and the experimental data is obtained, suggesting that the DEM can be used to predict large volumetric strains for clay sediments. It is also shown, through numerical simulations, that ionic strength of the pore fluid is an important controlling factor for volumetric strain. For low ionic strength, montmorillonite can experience a void ratio increase up to 2.0 compared with high ionic strengths. For ionic strength ranging from 0.001 to 2.0, changes in void ratio for montmorillonite are higher than kaolinite by a factor of two.