Line Active Hybrid Lipids Determine Domain Size in Phase Separation of Saturated and Unsaturated Lipids

A simple model of the line activity of a hybrid lipid (e.g., POPC) with one fully saturated chain and one partially unsaturated chain demonstrates that these lipids preferentially pack at curved interfaces between phase-separated saturated and unsaturated domains. We predict that the domain sizes typically range from tens to hundreds of nm, depending on molecular interactions and parameters such as molecular volume and area per headgroup in the bulk fluid phase. The role of cholesterol is taken into account by an effective change in the headgroup areas and the domain sizes are predicted to increase with cholesterol concentration.     

Distinctive Network Topology of Phase-Separated Proteins in Human Interactome

Liquid-liquid phase separation (LLPS) is an important mechanism that mediates the formation of biomolecular condensates. Despite the immense interest in LLPS, phase-separated proteins verified by experiments are still limited, and identification of phase-separated proteins at proteome-scale is a challenging task. Multivalent interaction among macromolecules is the driving force of LLPS, which suggests that phase-separated proteins may harbor distinct biological characteristics in protein–protein interactions (PPIs). In this study, we constructed an integrated human PPI network (HPIN) and mapped phase-separated proteins into it. Analysis of the network parameters revealed differences of network topology between phase-separated proteins and others. The results further suggested the efficiency when applying topological similarities in distinguishing components of MLOs. Furthermore, we found that affinity purification mass spectrometry (AP-MS) detects PPIs more effectively than yeast-two hybrid system (Y2H) in phase separation-driven condensates. Our work provides the first global view of the distinct network topology of phase-separated proteins in human interactome, suggesting incorporation of PPI network for LLPS prediction in further studies.     

Splicing at the phase-separated nuclear speckle interface: a model

Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of phase separation may play functional roles. Specifically, we propose that interfaces of phase-separated membraneless bodies could have functional roles in spatially organizing biochemical reactions. Here we propose such a model for the nuclear speckle, a membraneless body implicated in RNA splicing. In our model, sequence-dependent RNA positioning along the nuclear speckle interface coordinates RNA splicing. Our model asserts that exons are preferentially sequestered into nuclear speckles through binding by SR proteins, while introns are excluded through binding by nucleoplasmic hnRNP proteins. As a result, splice sites at exon-intron boundaries are preferentially positioned at nuclear speckle interfaces. This positioning exposes splice sites to interface-localized spliceosomes, enabling the subsequent splicing reaction. Our model provides a simple mechanism that seamlessly explains much of the complex logic of splicing. This logic includes experimental results such as the antagonistic duality between splicing factors, the position dependence of splicing sequence motifs, and the collective contribution of many motifs to splicing decisions. Similar functional roles for phase-separated interfaces may exist for other membraneless bodies.     

Rotational dynamics of curved DNA fragments studied by fluorescence polarization anisotropy

The rotational dynamics of short DNA fragments with or without intrinsic curvature were studied using time-resolved phase fluorimetry of intercalated ethidium with detection of the anisotropy. Parameters determined were the spinning diffusion coefficient of the DNA fragments about the long axis and the zero-time ethidium fluorescence anisotropy. We find a significant decrease in the spinning diffusion coefficient for all curved fragments compared to the straight controls. This decrease is likewise evident in rotational diffusion coefficients computed from DNA structures obtained by a curvature prediction program for these sequences. Using a hinged-cylinder model, we can identify the change in rotational diffusion coefficient with a permanent bend of 13-16 degrees per helix turn for the sequences studied. Moreover, for some of the curved fragments an increased flexibility has to be assumed in addition to the permanent bend in order to explain the data.     

Current voltage curves of biomolecular lipid membranes.

The first part of this paper describes the current voltage curves of bimolecular membranes of oxidized cholesterol formed between two aqueous solutions of tetrabutylammonium chloride. These membranes are selectively permeable for cations and the membrane interfaces are electrically uncharged. The dependence of the membrane conductivity on the membrane potential can be described as the product of the conductivity at zero current ("zero conductivity") and a function called "overlinearity". The zero conductivity increases linearly with the concentration of tetrabutylammonium chloride. The overlinearity is independent of the concentration of tetrabutylammonium chloride. In the second part the Nernst-Planck and Poisson equations are integrated numerically for a three-phase system consisting of an aqueous electrolyte solution, a membrane and an aqueous electrolyte solution. Each phase is characterized by material constants. Appropriate boundary conditions cause the electric current to build up electrical double layers on both sides of the membrane. The opposing double layers with opposite electrical signs inject the soluble ions into the membrane. This ion injection accounts for the overlinearity of the current voltage curves, thus explaining the measured characteristics.     

Compositional mapping of mixed gels using FTIR microspectroscopy

We have developed a technique to produce compositional maps of phase-separated protein/polysaccharide mixed gels using Fourier transform infrared (FTIR) microspectroscopy. The maps plot out the composition of either the protein, the polysaccharide or the water as a function of position in the sample and are presented in the form of two-dimensional contour plots. Our technique is completely general in nature, since it simply relies on there being some measurable spectral difference between the two biopolymers. However, in this paper we use our technique to study the particular case of aqueous gelatin/ amylopectin gels.

Semi-quantitative compositional maps were generated in the first instance by simply plotting the area of the infrared amide II absorption band from the gelatin. Fully quantitative compositional maps, in terms of actual weight percentage concentration of gelatin, amylopectin and water, were also produced by analysing a particular region of the spectra with the method of partial least-squares (PLS).

We recently showed how PLS analysis can be used in conjunction with FTIR spectroscopy to plot the phase diagram of bulk phase-separated solutions which are held above the gel temperature of both components. Thus, our mapping technique allows the concentrations in a gel to be directly compared with those reached at equilibrium in the bulk phase-separated solution, using the same molecular probe, namely, infrared radiation.     

Wettability of polymers by mucin aqueous solutions

The wettability of poly(methyl methacrylate) and polyethylene by water and aqueous mucin solutions have been studied by sessile drop and under-water captive air bubble contact angles, respectively. From the sessile drop and octane under-water contact angles the polymer-water interfaces have been characterized in terms of works of adhesion and acid-base (polar) interactions. A large water-air contact angle hysteresis observed with poly(methyl methacrylate) surfaces has been attributed to side-chain beta relaxations of polymer ester methyl groups. The wettabilities of the polymers by mucin aqueous solutions have been studied as a function of protein concentration and related to the surface tensions. A positive slope of adhesion tension vs surface tension line, characteristic of polar surfaces, was found with poly(methyl methacrylate). By contrast, a change in the slope, explained as a change in mucin relative adsorption densities at solid/liquid and solid/vapour interfaces, was observed with polyethylene. This adhesion tension behavior appeared to be in agreement with previous data we have published concerning the quantity and state of mucin which are adsorbed to polymers characterized by different surface properties.     

Concentration of mammalian genomic DNA using two‐phase aqueous micellar systems

The concentration of biomarkers, such as DNA, prior to a subsequent detection step may facilitate the early detection of cancer, which could significantly increase chances for survival. In this study, the partitioning behavior of mammalian genomic DNA fragments in a two‐phase aqueous micellar system was investigated using both experiment and theory. The micellar system was generated using the nonionic surfactant Triton X‐114 and phosphate‐buffered saline (PBS). Partition coefficients were measured under a variety of conditions and compared with our theoretical predictions. With this comparison, we demonstrated that the partitioning behavior of DNA fragments in this system is primarily driven by repulsive, steric, excluded‐volume interactions that operate between the micelles and the DNA fragments, but is limited by the entrainment of micelle‐poor, DNA‐rich domains in the macroscopic micelle‐rich phase. Furthermore, the volume ratio, that is, the volume of the top, micelle‐poor phase divided by that of the bottom, micelle‐rich phase, was manipulated to concentrate DNA fragments in the top phase. Specifically, by decreasing the volume ratio from 1 to 1/10, we demonstrated proof‐of‐principle that the concentration of DNA fragments in the top phase could be increased two‐ to nine‐fold in a predictive manner. Biotechnol. Bioeng. 2009;102: 1613–1623. © 2008 Wiley Periodicals, Inc.     

Self-assembling of polymer-enzyme conjugates at oil/water interfaces

Interface-binding enzymes are desirable for biphasic reactions in that they offer simultaneous access to substrates dissolved in both phases across the interface. It has been shown that conjugating water-soluble enzymes with hydrophobic polymers facilitated the assembling of enzymes at oil/water interfaces. In this work, the interfacial assembling of alpha-chymotrypsin conjugated with polystyrene, poly(methyl methacrylate), and poly(l-lactic acid) was examined using the pendant drop method. The interface-assembling process of the conjugates from the organic phase followed a similar pattern of that of native alpha-chymotrypsin from the aqueous buffer phase, i.e., the interfacial tension decreased gradually with time. However, when the conjugates were dispersed in the form of particulates in the aqueous phase, in which the conjugate was insoluble, the assembling occurred faster and the interfacial tension quickly approached zero. It was suspected that the assembling in this case involved two steps, i.e., the adsorption of the particulates and the subsequent rearrangement, dissociation, and redispersion of the conjugates at the interface. The effect of other factors, including the polarity of organic solvent and pH and ionic strength of the aqueous phase, was evaluated. It was found that the polar solvent slightly facilitated the assembling, whereas pH and ionic strength showed minimal effects.     

A novel approach to biotransformations in aqueous-organic two-phase systems: enzymatic synthesis of alkyl beta-[D]-glucosides using microencapsulated beta-glucosidase

A novel approach to enzymatic biotransformations in aqueous-organic two-phase systems was developed where the aqueous phase was contained within permeable polymeric capsules suspended in organic solvent. Microencapsulated beta-glucosidase, used as a model enzyme, was shown to retain its catalytic activity for a considerable time and was repeatedly used in batch experiments after recharging the microcapsules with solid glucose. The reaction conditions for the synthesis of hexyl beta-[D]-glucopyranoside were optimized with regard to the polymer composition of the microcapsules, pH, and the volume ratio of aqueous to organic phases. The potential for further improvement in the efficiency of the system was demonstrated by designing a bioreactor which incorporated units for product recovery and recycling of the organic solvent. Other advantages of the proposed methodology include facile control over the size and composition of the microcapsules, and mild reaction conditions during their preparation.     

Microwave-field-assisted enhanced demixing of aqueous two-phase systems

The slow rate of demixing is a major limitation in wide commercial exploitation of aqueous two-phase systems. In the present work, use of a microwave field has been explored for the first time to enhance phase demixing rates (decrease demixing times) of these systems. The microwave-field-assisted demixing process decreased the demixing time by about 2- to 4-fold in a polyethylene glycol/potassium phosphate system and by about 1.5- to 6.5-fold in a polyethylene glycol/maltodextrin system. The enhanced demixing rate can be explained by the dipole rotation, electrophoretic migration of free salts, multiple reflections at the interfaces, droplet-droplet collision, and reduced viscosity of the continuous phase that occur during the application of a microwave field.     

Molecular Dynamics Study of High Temperature Phase-Separation in a H2O/N2 Mixture with Exp-6 Interactions

Abstract

Equimolar H₂O/N₂ fluid mixture was studied by molecular dynamics simulations for NVT ensemble. Calculations were performed with the modified Buckingham (exp-6) potentials at T = 2000 K. Particular attention was given to the phase separation at very high pressures relevant to a detonation environment. Calculations of pair correlation functions and local mole fractions clearly indicated the occurrence of the fluid separation into N₂-rich and H₂O-rich phase. The density at the phase boundary between homogeneous and inhomogeneous phase-separated state was determined to be p = 1.35 g/cm³ on the basis of the static cross correlation factor which is defined by the sum of the local mole fractions. The ratio of the self-diffusion coefficients of N₂ and H₂O at p < 1.35 g/cm³ was found to be approximately equal to the value predicted by the kinetic theory of the ideal gas, whereas the ratio was close to unity at the phase-separated state (p > 1.35 g/cm³). In addition, two distinctive behaviors of the system could be observed for the relaxation from the initial uniform mixture to the phase-separated fluid: at lower densities (1.35 < p < 2.0 g/cm³) the fluid mixture began to relax into the phase-separated system without obvious incubation time, while clear incubation period was associated for the separation at higher densities. During this incubation period, discontinuous jumps in the mean square displacements were found.     

The internal aqueous volume of small unilamellar vesicles changes at the phase transition temperature of the phospholipid

Changes in the fluorescence of partially self-quenched 5(6)-carboxyfluorescein trapped within the internal aqueous compartment of small unilamellar dipalmitoylphosphatidylcholine vesicles indicate that the trapped volume of these vesicles decreases when the phospholipid undergoes the liquid crystalline to gel state transition. This volume change is completely reversible and is not caused by vesicle-vesicle fusion. Furthermore, this decrease in volume of the internal aqueous compartment may be attributed to a change in vesicle shape upon undergoing the phase transition.     

Biodegradation kinetics of naphthalene in nonaqueous phase liquid-water mixed batch systems: comparison of model predictions and experimental results

A model is formulated to describe dissolution of naphthalene from an insoluble nonaqueous phase liquid (NAPL) and its subsequent biodegradation in the aqueous phase in completely mixed batch reactors. The physicochemical processes of equilibrium partitioning and mass transfer of naphthalene between the NAPL and aqueous phases were incorporated into the model. Biodegradation kinetics were described by Monod's microbial growth kinetic model, modified to account for the inhibitory effects of 1,2-naphthoquinone formed during naphthalene degradation under certain conditions. System parameters and biokinetic coefficients pertinent to the NAPL-water systems were determined either by direct measurement or from nonlinear regression of the naphthalene mineralization profiles obtained from batch reactor tests with two-component NAPLs comprised of naphthalene and heptamethylnonane. The NAPLs contained substantial mass of naphthalene, and naphthalene biodegradation kinetics were evaluated over the time required for near complete depletion of naphthalene from the NAPL. Model predictions of naphthalene mineralization time profiles compared favorably to the general trends observed in the data obtained from laboratory experiments with the two-component NAPL, as well as with two coal tars obtained from the subsurface at contaminated sites and composed of many different PAHs (polycyclic aromatic hydrocarbon compounds). The effects of varying the NAPL mass and the naphthalene mole fractions in the NAPL are discussed. It was observed that the time to achieve a given percent removal of naphthalene does not change significantly with the initial mass of naphthalene in a fixed volume of the NAPL. Significant changes in the mineralization profiles are observed when the volume (and mass) of NAPL in the system is changed.     

Characterization of aqueous two-phase systems based on polydisperse phase forming polymers: Enzymatic hydrolysis of starch in a PEG-starch aqueous two-phase system

A new method for determination of the binodial of an aqueous two-phase system, using spectrophotometric measurements of the turbidity, is described in this article. The method is especially designed to characterize phase systems composed of polydisperse phase components. It gives information about the area representing the transition from homogeneous solution to a two-phase system. The two-phase systems studied were first a conventional Dextran T40-polyethylene glycol 20M (PEG 20M) system, then a less-well-defined phase system based on PEG 20M and partially hydrolyzed starch. The PEG 20M-starch system could be changed with respect to the volume ratio between the phases with time using hydrolytic enzymes, and the possibility of using the glucose released from the starch polymer is pointed out. Then the system is transformed to an extractive biconversion where the bottom phase polymer also served as the substrate.     

Kinetic theory of enzymatic reactions in reversed micellar systems. Application of the pseudophase approach for partitioning substrates

A kinetic theory is proposed for enzymatic reactions proceeding in reversed micellar systems in organic solvents, and involving substrates capable of partitioning among all pseudophases of the micellar system i.e. aqueous cores of reversed micelles, micellar membranes and organic solvent. The theory permits determination of true (i.e. with reference to the aqueous phase, where solubilized enzyme is localized) catalytic parameters of the enzyme, provided partition coefficients of the substrate between different phases are known. The validity of the kinetic theory was verified by the example of oxidation of aliphatic alcohols catalyzed by horse liver alcohol dehydrogenase in the system of reversed sodium bis(2-ethylhexyl)sulfosuccinate (AOT, aerosol OT) micelles in octane. In order to determine partition coefficients of alcohols between phases of the micellar system, flow microcalorimetry technique was used. It was shown that in the first approximation, the partition coefficient of the substrate in a simple biphasic system consisting of water and corresponding organic solvent can be used as an estimate for the partition coefficient of the substrate between aqueous and organic solvent phases of the micellar system. True values of the Michaelis constant of alcohols in the micellar system, determined using suggested approach, are equal to those obtained in aqueous solution and differ from apparent values referred to the total volume of the system. The results clearly show that the previously reported shift in the substrate specificity of HLADH, observed on changing from aqueous solution to the system of reversed aerosol OT micelles in octane, is apparent and can be explained on the basis of partitioning effects of alcoholic substrates between phases of the micellar system.     

A quantitative dynamic concept of the interphase partition of lipids: application to bile salt-lecithin-cholesterol mixed micelles

A system is proposed for a quantitative classification of lipids, based on interphase partition coefficients. This system enables calculation of exchanges of lipid molecules between phases. The mass/volume chemical unit mol X cm-3, strictly derived from the CGS system, is used, thus simplifying mathematical relations. Applied to bile salt-lecithin-cholesterol mixed micelles, this dynamic concept gives new insight into the variations of physico-chemical parameters. Experimental results obtained with the glycodesoxycholate and the taurocholate show a striking difference in partition coefficients between aqueous and mixed bile salt-lecithin interfacial phases. A new model applying triangular co-ordinates to a bile salt-lecithin-cholesterol mixed lipid phase is described.