Open resources for chemical probes and their implications for future drug discovery

INTRODUCTION

The rational development of new therapeutics requires a thorough understanding of how aberrant signalling affects cellular homeostasis and causes human disease. Chemical probes are tool compounds with well-defined mechanism-of-action enabling modulation of, for example, domain-specific protein properties in a temporal manner, thereby complementing other target validation methods such as genetic gain- and loss-of-function approaches.

AREAS COVERED

In this review, the authors summarize recent advances in chemical probe development for emerging target classes such as solute carriers and ubiquitin-related targets and highlight open resources to inform and facilitate chemical probe discovery as well as tool compound selection for target validation and phenotypic screening.

EXPERT OPINION

Chemical probes are powerful tools for drug discovery that have led to fundamental insights into biological processes and have paved the way for the development of first-in-class drugs. Open resources can inform on various aspects of chemical probe development and provide access to data and recommendations on use of chemical probes to catalyse collaborative science and help accelerate drug target identification and validation.

Microfluidic-Derived Detection of Protein-Facilitated Copper Flux Across Lipid Membranes

Measurement of protein-facilitated copper flux across biological membranes is a considerable challenge. Here, we demonstrate a straightforward microfluidic-derived approach for visualization and measurement of membranous Cu flux. Giant unilamellar vesicles, reconstituted with the membrane protein of interest, are prepared, surface-immobilized, and assessed using a novel quencher–sensor reporter system for detection of copper. With the aid of a syringe pump, the external buffer is exchanged, enabling consistent and precise exchange of solutes, without causing vesicle rupture or uneven local metal concentrations brought about by rapid mixing. This approach bypasses common issues encountered when studying heavy metal-ion flux, thereby providing a new platform for in vitro studies of metal homeostasis aspects that are critical for all cells, health, and disease.

Aquaglyceroporins and orthodox aquaporins in human adipocytes

Aquaporins play a crucial role in water homeostasis in the human body, and recently the physiological importance of aquaporins as glycerol channels have been demonstrated. The aquaglyceroporins (AQP3, AQP7, AQP9 and AQP10) represent key glycerol channels, enabling glycerol flux across the membranes of cells. Adipocytes are the major source of glycerol and during lipolysis, glycerol is released to be metabolized by other tissues through a well-orchestrated process. Here we show that both AQP3 and AQP7 bind to the lipid droplet protein perilipin 1 (PLIN1), suggesting that PLIN1 is involved in the coordination of the subcellular translocation of aquaglyceroporins in human adipocytes. Moreover, in addition to aquaglyceroporins, we discovered by transcriptome sequencing that AQP1 is expressed in human primary adipocytes. AQP1 is mainly a water channel and thus is thought to be involved in the response to hyper-osmotic stress by efflux of water during hyperglycemia. Thus, this data suggests a contribution of both orthodox aquaporin and aquaglyceroporin in human adipocytes to maintain the homeostasis of glycerol and water during fasting and feeding.

Generalized hydrodynamics of the Lennard-Jones liquid in view of hidden scale invariance

In recent years lines along which structure and dynamics are invariant to a good approximation, so-called isomorphs, have been identified in the thermodynamic phase diagrams of several model liquids and solids. This paper reports computer simulation data of the transverse and longitudinal collective dynamics at different length scales along an isomorph of the Lennard-Jones system. Our findings are compared to corresponding results along an isotherm and an isochore. Confirming the theoretical prediction, the reduced-unit dynamics of the transverse momentum density is invariant to a good approximation along the isomorph on all time and length scales. Likewise, the wave-vector dependent shear-stress autocorrelation function is found to be isomorph invariant (with minor deviations at very short times). A similar invariance is not seen along the isotherm or the isochore. Using a spatially nonlocal hydrodynamic model for the transverse momentum-density time-autocorrelation function, the macroscopic shear viscosity and its wave dependence are determined, demonstrating that the shear viscosity is isomorphic invariant on all length scales studied. This analysis implies the existence of a length scale that is isomorph invariant in reduced units, i.e., which characterizes each isomorph. The transverse sound-wave velocity, the Maxwell relaxation time, and the rigidity shear modulus are also isomorph invariant. In contrast to the isomorph invariance of all aspects of the transverse dynamics, the reduced-unit dynamics of the mass density is not invariant on length scales longer than the interparticle distance. By fitting to a generalized hydrodynamic model, we extract values for the wave-vector-dependent thermal diffusion coefficient, sound attenuation coefficient, and adiabatic sound velocity. The isomorph variation of these quantities in reduced units on long length scales can be eliminated by scaling with the density-scaling exponent, a fundamental quantity in the isomorph theory framework; this is an empirical observation that remains to be explained theoretically.

Electropumping of nanofluidic water by linear and angular momentum coupling: theoretical foundations and molecular dynamics simulations

In this article we review the relatively new phenomenon of electropumping in nanofluidic systems, in which nonzero net flow results when polar molecules are rotated by external electric fields. The flow is a consequence of coupling of the spin angular momentum of molecules with their linear streaming momentum. By devising confining surfaces that are asymmetric - specifically one surface is more hydrophobic compared to the other - unidirectional flow results and so pumping can be achieved without the use of pressure gradients. We first cover the historical background to this phenomenon and follow that with a detailed theoretical description of the governing hydrodynamics. Following that we summarise work that has applied this phenomenon to pump water confined to planar nanochannels, semi-functionalised single carbon nanotubes and concentric carbon nanotubes. We also report on the energy efficiency of this pumping technique by comparisons with traditional flows of planar Couette and Poiseuille flow, with the surprising conclusion that electropumping at the nanoscale is some 4 orders of magnitude more efficient than pumping by Poiseuille flow.

Slow lactate gluconate exchange in calcium complexes during precipitation from supersaturated aqueous solutions

Saturated solutions of calcium l-lactate in water or in deuterium oxide continuously dissolve calcium l-lactate by addition of solid sodium d-gluconate and become strongly supersaturated in calcium d-gluconate due to no or slow precipitation. The quantification of total dissolved calcium allied with the calcium complexes equilibrium constants allowed an ion speciation, which shows an initial non-thermal and spontaneous supersaturation of more than a factor of 50 at 25 °C only slowly decreasing after initiation of precipitation of calcium d-gluconate after a lag phase of several hours. A mathematical model is proposed, based on numerical solution of coupled differential equations of dynamics of l-lactate and d-gluconate exchange during the lag phase for precipitation and during precipitation. A slow exchange of l-lactate coordinated to calcium with d-gluconate is indicated with a time constant of 0.20 h^-1 in water and of 0.15 h^-1 in deuterium oxide and a kinetic deuterium/hydrogen isotope effect of 1.25. Such spontaneous non-thermal supersaturation and slow ligand exchange with a pseudo first order equilibration process with a half-life of 3.5 h in water for calcium hydroxycarboxylates can help to understand the higher calcium bioavailability from calcium hydroxycarboxylates compared to simple salts.

Peptide-Oleate Complexes Create Novel Membrane-Bound Compartments

A challenging question in evolutionary theory is the origin of cell division and plausible molecular mechanisms involved. Here, we made the surprising observation that complexes formed by short alpha-helical peptides and oleic acid can create multiple membrane-enclosed spaces from a single lipid vesicle. The findings suggest that such complexes may contain the molecular information necessary to initiate and sustain this process. Based on these observations, we propose a new molecular model to understand protocell division.

Probable Post-traumatic Stress Disorder and Self-harming Behaviour: Potential Barriers to Employment?

The current study screened for post-traumatic stress disorder (PTSD) and self-harming behaviours, often related to borderline personality disorder (BPD), among individuals in a job centre considered unemployable primarily for psychological reasons. Participants (N = 112) filled in questionnaires on PTSD symptoms (n = 62) and self-harming behaviours (n = 59) as part of participating in team-meetings providing the individuals with a return-to-work plan. Differences in demographic variables between individuals with and without valid protocols were small to moderate. Of the individuals filling in the PTSD questionnaire 40% fulfilled criteria for probable PTSD and 31% of the individuals filling in the questionnaire on self-harming behaviours reported five or more types of self-harming behaviours. Only a minority of these individuals had PTSD or BPD respectively mentioned in their case records. Further investigation of the prevalence of PTSD and self-harming behaviour among individuals considered unemployable is warranted as well as an enhanced focus in jobcentres and other institutions supporting employability on detection and treatment of PTSD and early signs of BPD.

Quantification of the Intracellular Life Time of Water Molecules to Measure Transport Rates of Human Aquaglyceroporins

Orthodox aquaporins are transmembrane channel proteins that facilitate rapid diffusion of water, while aquaglyceroporins facilitate the diffusion of small uncharged molecules such as glycerol and arsenic trioxide. Aquaglyceroporins play important roles in human physiology, in particular for glycerol metabolism and arsenic detoxification. We have developed a unique system applying the strain of the yeast Pichia pastoris, where the endogenous aquaporins/aquaglyceroporins have been removed and human aquaglyceroporins AQP3, AQP7, and AQP9 are recombinantly expressed enabling comparative permeability measurements between the expressed proteins. Using a newly established Nuclear Magnetic Resonance approach based on measurement of the intracellular life time of water, we propose that human aquaglyceroporins are poor facilitators of water and that the water transport efficiency is similar to that of passive diffusion across native cell membranes. This is distinctly different from glycerol and arsenic trioxide, where high glycerol transport efficiency was recorded.

Correction: Thermal stability and structural changes in bacterial toxins responsible for food poisoning

[This corrects the article DOI: 10.1371/journal.pone.0172445.].

Thermal stability and structural changes in bacterial toxins responsible for food poisoning

The staphylococcal enterotoxins (SEs) are secreted by the bacteria Staphylococcus aureus and are the most common causative agent in staphylococcal food poisoning. The staphylococcal enterotoxin A (SEA) has been associated with large staphylococcal food poisoning outbreaks, but newer identified SEs, like staphylococcal enterotoxin H (SEH) has recently been shown to be present at similar levels as SEA in food poisoning outbreaks. Thus, we set out to investigate the thermo-stability of the three-dimensional structures of SEA, SEH and staphylococcal enterotoxin E (SEE), since heat inactivation is a common method to inactivate toxins during food processing. Interestingly, the investigated toxins behaved distinctly different upon heating. SEA and SEE were more stable at slightly acidic pH values, while SEH adopted an extremely stable structure at neutral pH, with almost no effects on secondary structural elements upon heating to 95°C, and with reversible formation of tertiary structure upon subsequent cooling to room temperature. Taken together, the data suggests that the family of staphylococcal enterotoxins have different ability to withstand heat, and thus the exact profile of heat inactivation for all SEs causing food poisoning needs to be considered to improve food safety.

Liver and Muscle Contribute Differently to the Plasma Acylcarnitine Pool During Fasting and Exercise in Humans

BACKGROUND

Plasma acylcarnitine levels are elevated by physiological conditions such as fasting and exercise but also in states of insulin resistance and obesity.

AIM

To elucidate the contribution of liver and skeletal muscle to plasma acylcarnitines in the fasting state and during exercise in humans.

METHODS

In 2 independent studies, young healthy males were fasted overnight and performed an acute bout of exercise to investigate either acylcarnitines in skeletal muscle biopsies and arterial-to-venous plasma differences over the exercising and resting leg (n = 9) or the flux over the hepato-splanchnic bed (n = 10).

RESULTS

In the fasting state, a pronounced release of C2- and C3-carnitines from the hepato-splanchnic bed and an uptake of free carnitine by the legs were detected. Exercise further increased the release of C3-carnitine from the hepato-splanchnic bed and the uptake of free carnitine in the exercising leg. In plasma and in the exercising muscle, exercise induced an increase of most acylcarnitines followed by a rapid decline to preexercise values during recovery. In contrast, free carnitine was decreased in the exercising muscle and quickly restored thereafter. C8-, C10-, C10:1-, C12-, and C12:1-carnitines were released from the exercising leg and simultaneously; C6, C8, C10, C10:1, C14, and C16:1 were taken up by the hepato-splanchnic.

CONCLUSION

These data provide novel insight to the organo-specific release/uptake of acylcarnitines. The liver is a major contributor to systemic short chain acylcarnitines, whereas the muscle tissue releases mostly medium chain acylcarnitines during exercise, indicating that other tissues are contributing to the systemic increase in long chain acylcarnitines.

Perilipin 1 binds to aquaporin 7 in human adipocytes and controls its mobility via protein kinase A mediated phosphorylation

Accumulating evidence suggests that dysregulated glycerol metabolism contributes to the pathophysiology of obesity and type 2 diabetes. Glycerol efflux from adipocytes is regulated by the aquaglyceroporin AQP7, which is translocated upon hormone stimulation. Here, we propose a molecular mechanism where the AQP7 mobility in adipocytes is dependent on perilipin 1 and protein kinase A. Biochemical analyses combined with ex vivo studies in human primary adipocytes, demonstrate that perilipin 1 binds to AQP7, and that catecholamine activated protein kinase A phosphorylates the N-terminus of AQP7, thereby reducing complex formation. Together, these findings are indicative of how glycerol release is controlled in adipocytes, and may pave the way for the future design of drugs against human metabolic pathologies.

Identification of Structural Relaxation in the Dielectric Response of Water

One century ago pioneering dielectric results obtained for water and n-alcohols triggered the advent of molecular rotation diffusion theory considered by Debye to describe the primary dielectric absorption in these liquids. Comparing dielectric, viscoelastic, and light scattering results, we unambiguously demonstrate that the structural relaxation appears only as a high-frequency shoulder in the dielectric spectra of water. In contrast, the main dielectric peak is related to a supramolecular structure, analogous to the Debye-like peak observed in monoalcohols.

Effect of chenodeoxycholic acid and the bile acid sequestrant colesevelam on glucagon-like peptide-1 secretion

AIM

To evaluate the effects of the primary human bile acid, chenodeoxycholic acid (CDCA), and the bile acid sequestrant (BAS) colesevelam, instilled into the stomach, on plasma levels of glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic polypeptide, glucose, insulin, C-peptide, glucagon, cholecystokinin and gastrin, as well as on gastric emptying, gallbladder volume, appetite and food intake.

METHODS

On four separate days, nine patients with type 2 diabetes, and 10 matched healthy control subjects received bolus instillations of (i) CDCA, (ii) colesevelam, (iii) CDCA + colesevelam or (iv) placebo. At baseline and for 180 min after instillation, blood was sampled.

RESULTS

In both the type 2 diabetes group and the healthy control group, CDCA elicited an increase in GLP-1 levels compared with colesevelam, CDCA + colesevelam and placebo, respectively (p < 0.05). The interventions did not affect plasma glucose, insulin or C-peptide concentrations in any of the groups. CDCA elicited a small increase in plasma insulin : glucose ratio compared with colesevelam, CDCA + colesevelam and placebo in both groups. Compared with colesevelam, CDCA + colesevelam and placebo, respectively, CDCA increased glucagon and delayed gastric emptying in both groups.

CONCLUSIONS

CDCA increased GLP-1 and glucagon secretion, and delayed gastric emptying. We speculate that bile acid-induced activation of TGR5 on L cells increases GLP-1 secretion, which, in turn, may result in amplification of glucose-stimulated insulin secretion. Furthermore our data suggest that colesevelam does not have an acute effect on GLP-1 secretion in humans.

Effects of Confinement on the Dielectric Response of Water Extends up to Mesoscale Dimensions

The extent of confinement effects on water is not clear in the literature. While some properties are affected only within a few nanometers from the wall surface, others are affected over long length scales, but the range is not clear. In this work, we have examined the dielectric response of confined water under the influence of external electric fields along with the dipolar fluctuations at equilibrium. The confinement induces a strong anisotropic effect which is evident up to 100 nm channel width, and may extend to macroscopic dimensions. The root-mean-square fluctuations of the total orientational dipole moment in the direction perpendicular to the surfaces is 1 order of magnitude smaller than the value attained in the parallel direction and is independent of the channel width. Consequently, the isotropic condition is unlikely to be recovered until the channel width reaches macroscopic dimensions. Consistent with dipole moment fluctuations, the effect of confinement on the dielectric response also persists up to channel widths considerably beyond 100 nm. When an electric field is applied in the perpendicular direction, the orientational relaxation is 3 orders of magnitude faster than the dipolar relaxation in the parallel direction and independent of temperature.

Finite-size effects in a model for plasticity of amorphous composites

We discuss the plastic behavior of an amorphous matrix reinforced by hard particles. A mesoscopic depinning-like model accounting for Eshelby elastic interactions is implemented. Only the effect of a plastic disorder is considered. Numerical results show a complex size dependence of the effective flow stress of the amorphous composite. In particular, the departure from the mixing law shows opposite trends associated to the competing effects of the matrix and the reinforcing particles, respectively. The reinforcing mechanisms and their effects on localization are discussed. Plastic strain is shown to gradually concentrate on the weakest band of the system. This correlation of the plastic behavior with the material structure is used to design a simple analytical model. The latter nicely captures reinforcement size effects in (logN/N)(1/2), where N is the linear size of the system, observed numerically. Predictions of the effective flow stress accounting for further logarithmic corrections show a very good agreement with numerical results.

Continuum Nanofluidics

This paper introduces the fundamental continuum theory governing momentum transport in isotropic nanofluidic systems. The theory is an extension of the classical Navier-Stokes equation, and includes coupling between translational and rotational degrees of freedom as well as nonlocal response functions that incorporate spatial correlations. The continuum theory is compared with molecular dynamics simulation data for both relaxation processes and fluid flows, showing excellent agreement on the nanometer length scale. We also present practical tools to estimate when the extended theory should be used. It is shown that in the wall-fluid region the fluid molecules align with the wall, and in this region the isotropic model may fail and a full anisotropic description is necessary.

Simple Statistical Model for Branched Aggregates: Application to Cooee Bitumen

We propose a statistical model that can reproduce the size distribution of any branched aggregate, including amylopectin, dendrimers, molecular clusters of monoalcohols, and asphaltene nanoaggregates. It is based on the conditional probability for one molecule to form a new bond with a molecule, given that it already has bonds with others. The model is applied here to asphaltene nanoaggregates observed in molecular dynamics simulations of Cooee bitumen. The variation with temperature of the probabilities deduced from this model is discussed in terms of statistical mechanics arguments. The relevance of the statistical model in the case of asphaltene nanoaggregates is checked by comparing the predicted value of the probability for one molecule to have exactly i bonds with the same probability directly measured in the molecular dynamics simulations. The agreement is satisfactory.

Glucose transport machinery reconstituted in cell models

Here we demonstrate the production of a functioning cell model by formation of giant vesicles reconstituted with the GLUT1 glucose transporter and a glucose oxidase and hydrogen peroxidase linked fluorescent reporter internally. Hence, a simplified artificial cell is formed that is able to take up glucose and process it.

Nanoscale Turing structures

Formation of Turing patterns of nanoscopic length scale is simulated using molecular dynamics. Based on Fourier spectra of the concentrations of species, we compare stabilities of the structures of different wavelengths and for different intermolecular potentials. Long range attraction is shown to oppose the formation of structures. Our simulations suggest that Turing patterns can be a method of self-organization at a length scale of down to 20 molecular diameters.

Preparation of size tunable giant vesicles from cross-linked dextran(ethylene glycol) hydrogels

We present a novel chemically cross-linked dextran-poly(ethylene glycol) hydrogel substrate for the preparation of dense vesicle suspensions under physiological ionic strength conditions. These vesicles can be easily diluted for individual study. Modulating the degree of cross-linking within the hydrogel network results in tuning of the vesicle size distribution.

Pulmonary toxicity following exposure to a tile coating product containing alkylsiloxanes. A clinical and toxicological evaluation

CONTEXT

Coating products are widely used for making surfaces water and dirt repellent. However, on several occasions the use of these products has been associated with lung toxicity.

OBJECTIVE

In the present study, we evaluated the toxic effects of an aerosolized tile-coating product.

METHODS

Thirty-nine persons, who reported respiratory and systemic symptoms following exposure to the tile-coating product, were clinically examined. The product was analysed chemically and furthermore, the exposure scenario was reconstructed using a climate chamber and the toxicological properties of the product were studied using in vivo and by in vitro surfactometry.

RESULTS

The symptoms developed within few hours and included coughing, tachypnoea, chest pain, general malaise and fever. The physical examination revealed perihilar lung infiltrates on chest radiograph and reduced blood oxygen saturation. The acute symptoms resolved gradually within 1-3 days and no delayed symptoms were observed. By means of mass spectrometry and X-ray spectroscopy, it was shown that the product contained non-fluorinated alkylsiloxanes. The exposure conditions in the supermarket were reconstructed under controlled conditions in a climate chamber and particle and gas exposure levels were monitored over time allowing estimation of human exposure levels. Mice exposed to the product developed symptoms of acute pulmonary toxicity in a concentration-and time-dependent manner. The symptoms of acute pulmonary toxicity likely resulted from inhibition of the pulmonary surfactant function as demonstrated by in vitro surfactometry. Among these patients only a partial association between the level of exposure and the degree of respiratory symptoms was observed, which could be because of a high inter-individual difference in sensitivity and time-dependent changes in the chemical composition of the aerosol.

CONCLUSION

Workers need to cautiously apply surface coating products because the contents can be highly toxic through inhalation, and the aerosols can disperse to locations remote from the worksite and affect bystanders.

Molecular dynamics study of nanoconfined water flow driven by rotating electric fields under realistic experimental conditions

In our recent work, J. Chem. Phys. 2013, 138, 154712, we demonstrated the feasibility of unidirectional pumping of water, exploiting translational-rotational momentum coupling using nonequilibrium molecular dynamics simulations. Flow can be sustained when the fluid is driven out of equilibrium by an external spatially uniform rotating electric field and confined between two planar surfaces exposing different degrees of hydrophobicity. The permanent dipole moment of water follows the rotating field, thus inducing the molecules to spin, and the torque exerted by the field is continuously injected into the fluid, enabling a steady conversion of spin angular momentum into linear momentum. The translational-rotational coupling is a sensitive function of the rotating electric field parameters. In this work, we have found that there exists a small energy dissipation region attainable when the frequency of the rotating electric field matches the inverse of the dielectric relaxation time of water and when its amplitude lies in a range just before dielectric saturation effects take place. In this region, that is, when the frequency lies in a small window of the microwave region around ∼20 GHz and amplitude ∼0.03 V Å(-1), the translational-rotational coupling is most effective, yielding fluid velocities of magnitudes of ∼2 ms(-1) with only moderate fluid heating. In this work, we also confine water to a realistic nanochannel made of graphene giving a hydrophobic surface on one side and β-cristobalite giving a hydrophilic surface on the other, reproducing slip-and-stick velocity boundary conditions, respectively. This enables us to demonstrate that in a realistic environment, the coupling can be effectively exploited to achieve noncontact pumping of water at the nanoscale. A quantitative comparison between nonequilibrium molecular dynamics and analytical solutions of the extended Navier-Stokes equations, including an external rotating electric field has been performed, showing excellent agreement when the electric field parameters match the aforementioned small energy dissipation region.

Lipid directed intrinsic membrane protein segregation

We demonstrate a new approach for direct reconstitution of membrane proteins during giant vesicle formation. We show that it is straightforward to create a tissue-like giant vesicle film swelled with membrane protein using aquaporin SoPIP2;1 as an illustration. These vesicles can also be easily harvested for individual study. By controlling the lipid composition we are able to direct the aquaporin into specific immiscible liquid domains in giant vesicles. The oligomeric α-helical protein cosegregates with the cholesterol-poor domains in phase separating ternary mixtures.

Electropumping of water with rotating electric fields

Pumping of fluids confined to nanometer dimension spaces is a technically challenging yet vitally important technological application with far reaching consequences for lab-on-a-chip devices, biomimetic nanoscale reactors, nanoscale filtration devices and the like. All current pumping mechanisms require some sort of direct intrusion into the nanofluidic system, and involve mechanical or electronic components. In this paper, we present the first nonequilibrium molecular dynamics results to demonstrate that non-intrusive electropumping of liquid water on the nanoscale can be performed by subtly exploiting the coupling of spin angular momentum to linear streaming momentum. A spatially uniform rotating electric field is applied to water molecules, which couples to their permanent electric dipole moments. The resulting molecular rotational momentum is converted into linear streaming momentum of the fluid. By selectively tuning the degree of hydrophobicity of the solid walls one can generate a net unidirectional flow. Our results for the linear streaming and angular velocities of the confined water are in general agreement with the extended hydrodynamical theory for this process, though also suggest refinements to the theory are required. These numerical experiments confirm that this new concept for pumping of polar nanofluids can be employed under laboratory conditions, opening up significant new technological possibilities.

Effects of nanoscale density inhomogeneities on shearing fluids

It is well known that density inhomogeneities at the solid-liquid interface can have a strong effect on the velocity profile of a nanoconfined fluid in planar Poiseuille flow. However, it is difficult to control the density inhomogeneities induced by solid walls, making this type of system unsuitable for a comprehensive study of the effect on density inhomogeneity on nanofluidic flow. In this paper, we employ an external force compatible with periodic boundary conditions to induce the density variation, which greatly simplifies the problem when compared to flow in nonperiodic nanoconfined systems. Using the sinusoidal transverse force method to produce shearing velocity profiles and the sinusoidal longitudinal force method to produce inhomogeneous density profiles, we are able to observe the interactions between the two property inhomogeneities at the level of individual Fourier components. This gives us a method for direct measurement of the coupling between the density and velocity fields and allows us to introduce various feedback control mechanisms which customize fluid behavior in individual Fourier components. We briefly discuss the role of temperature inhomogeneity and consider whether local thermal expansion due to nonuniform viscous heating is sufficient to account for shear-induced density inhomogeneities. We also consider the local Newtonian constitutive relation relating the shear stress to the velocity gradient and show that the local model breaks down for sufficiently large density inhomogeneities over atomic length scales.

Generalized extended Navier-Stokes theory: multiscale spin relaxation in molecular fluids

This paper studies the relaxation of the molecular spin angular velocity in the framework of generalized extended Navier-Stokes theory. Using molecular dynamics simulations, it is shown that for uncharged diatomic molecules the relaxation time decreases with increasing molecular moment of inertia per unit mass. In the regime of large moment of inertia the fast relaxation is wave-vector independent and dominated by the coupling between spin and the fluid streaming velocity, whereas for small inertia the relaxation is slow and spin diffusion plays a significant role. The fast wave-vector-independent relaxation is also observed for highly packed systems. The transverse and longitudinal spin modes have, to a good approximation, identical relaxation, indicating that the longitudinal and transverse spin viscosities have same value. The relaxation is also shown to be isomorphic invariant. Finally, the effect of the coupling in the zero frequency and wave-vector limit is quantified by a characteristic length scale; if the system dimension is comparable to this length the coupling must be included into the fluid dynamical description. It is found that the length scale is independent of moment of inertia but dependent on the state point.

How fast does water flow in carbon nanotubes?

The purpose of this paper is threefold. First, we review the existing literature on flow rates of water in carbon nanotubes. Data for the slip length which characterizes the flow rate are scattered over 5 orders of magnitude for nanotubes of diameter 0.81-10 nm. Second, we precisely compute the slip length using equilibrium molecular dynamics (EMD) simulations, from which the interfacial friction between water and carbon nanotubes can be found, and also via external field driven non-equilibrium molecular dynamics simulations (NEMD). We discuss some of the issues in simulation studies which may be reasons for the large disagreements reported. By using the EMD method friction coefficient to determine the slip length, we overcome the limitations of NEMD simulations. In NEMD simulations, for each tube we apply a range of external fields to check the linear response of the fluid to the field and reliably extrapolate the results for the slip length to values of the field corresponding to experimentally accessible pressure gradients. Finally, we comment on several issues concerning water flow rates in carbon nanotubes which may lead to some future research directions in this area.

Generalized extended Navier-Stokes theory: correlations in molecular fluids with intrinsic angular momentum

The extended Navier-Stokes theory accounts for the coupling between the translational and rotational molecular degrees of freedom. In this paper, we generalize this theory to non-zero frequencies and wavevectors, which enables a new study of spatio-temporal correlation phenomena present in molecular fluids. To discuss these phenomena in detail, molecular dynamics simulations of molecular chlorine are performed for three different state points. In general, the theory captures the behavior for small wavevector and frequencies as expected. For example, in the hydrodynamic regime and for molecular fluids with small moment of inertia like chlorine, the theory predicts that the longitudinal and transverse intrinsic angular velocity correlation functions are almost identical, which is also seen in the molecular dynamics simulations. However, the theory fails at large wavevector and frequencies. To account for the correlations at these scales, we derive a phenomenological expression for the frequency dependent rotational viscosity and wavevector and frequency dependent longitudinal spin viscosity. From this we observe a significant coupling enhancement between the molecular angular velocity and translational velocity for large frequencies in the gas phase; this is not observed for the supercritical fluid and liquid state points.

Suppression of allergen-specific IgE in offspring after preconceptional immunisation: maternal, paternal and genetic influences

Immunisation of female mice with the allergen ovalbumin (OVA) during pregnancy reduces the OVA-specific IgE response in adult offspring. To approach primary prevention strategies for allergy, we investigated to what extent genetic, paternal and maternal factors influence this suppressive effect on allergic sensitisation in offspring and investigated the possibility of pregestational immunisation. Maternal allergen immunisation reduced OVA-specific IgE levels in immunised offspring, even after maternal immunisation up to 8 weeks before conception without further allergen exposure. Immunisation of immunodeficient BALB/c severe combined immune deficiency (SCID) dams mated with wild type males did not lead to IgE suppression in offspring, indicating the importance of a functional maternal immune system. Immunisation of male mice before the relevant spermatogenesis did not cause antibody suppression in offspring. OVA-specific IgG1, presumably of maternal origin, was present in naïve offspring only from immunised dams and was associated with suppressed IgE responses after offspring immunisation. The IgE-suppressive effect of maternal immunisation was demonstrated in all three immunocompetent strains tested (NIH/OlaHsd, BALB/cA and C57BL/6 mice). In conclusion, suppression of allergen-specific IgE production in offspring could not be induced by paternal immunisation, and genetic factors were of minor importance. In contrast, we demonstrate the necessity of maternal factors, possibly allergen-specific IgG1, resulting from a functional adaptive immune response, for the IgE-suppressive effect in offspring. These maternal factors could be induced by immunisation of female mice even before conception.

Do the repulsive and attractive pair forces play separate roles for the physics of liquids?

According to standard liquid-state theory repulsive and attractive pair forces play distinct roles for the physics of liquids. This paradigm is put into perspective here by demonstrating a continuous series of pair potentials that have virtually the same structure and dynamics, although only some of them have attractive forces of significance. Our findings reflect the fact that the motion of a given particle is determined by the total force on it, whereas the quantity usually discussed in liquid-state theory is the individual pair force.

Nonlocal viscosity kernel of mixtures

In this Brief Report we investigate the multiscale hydrodynamical response of a liquid as a function of mixture composition. This is done via a series of molecular dynamics simulations in which the wave-vector-dependent viscosity kernel is computed for three mixtures, each with 7-15 different compositions. We observe that the viscosity kernel is dependent on composition for simple atomic mixtures for all the wave vectors studied here; however, for a molecular mixture the kernel is independent of composition for large wave vectors. The deviation from ideal mixing is also studied. Here it is shown that the Lorentz-Berthelot interaction rule follows ideal mixing surprisingly well for a large range of wave vectors, whereas for both the Kob-Andersen and molecular mixtures large deviations are found. Furthermore, for the molecular system the deviation is wave-vector dependent such that there exists a characteristic correlation length scale at which the ideal mixing goes from underestimating to overestimating the viscosity.

Formation of giant protein vesicles by a lipid cosolvent method

This paper describes a method to create giant protein vesicles (GPVs) of ≥10 μm by solvent-driven fusion of large vesicles (0.1-0.2 μm) with reconstituted membrane proteins. We found that formation of GPVs proceeded from rotational mixing of protein-reconstituted large unilamellar vesicles (LUVs) with a lipid-containing solvent phase. We made GPVs by using n-decane and squalene as solvents, and applied generalized polarization (GP) imaging to monitor the polarity around the protein transmembrane region of aquaporins labeled with the polarity-sensitive probe Badan. Specifically, we created GPVs of spinach SoPIP2;1 and E. coli AqpZ aquaporins. Our findings show that hydrophobic interactions within the bilayer of formed GPVs are influenced not only by the solvent partitioning propensity, but also by lipid composition and membrane protein isoform.

Nanoflow hydrodynamics

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom.

Nitrogen dioxide: no influence on allergic sensitization in an intranasal mouse model with ovalbumin and diesel exhaust particles

The role of traffic-related air pollution in the development of allergic diseases is still unclear. We therefore investigated if NO₂, an important constituent of traffic-related air pollution, promotes allergic sensitization to the allergen ovalbumin (OVA). We also examined if NO₂ influenced the allergy adjuvant activity of diesel exhaust particles (DEP). For this purpose, mice were exposed intranasally to OVA with or without DEP present, immediately followed by exposure to NO₂ (5 or 25 parts per million [ppm]) or room air for 4 h in whole body exposure chambers. Eighteen hours after the last of three exposures, the lungs of half of the animals were lavaged with saline and markers of lung damage and lung inflammation in the bronchoalveolar lavage fluid (BALF) were measured. Three weeks later, after intranasal booster immunizations with OVA, the levels of OVA-specific IgE and IgG2a antibodies in serum were determined. Both NO₂ (25 ppm) and DEP gave lung damage, measured as increased total protein concentration in BALF, whereas only NO₂ seemed to stimulate release of the proinflammatory cytokine tumor necrosis factor alpha (TNF-α). In contrast, only DEP significantly increased the number of neutrophils. Furthermore, DEP in combination with OVA stimulated the production of serum allergen-specific IgE antibodies. NO₂, however, neither increased the production of allergen-specific IgE antibodies, nor influenced the IgE adjuvant activity of DEP. Thus, based on our findings, NO₂ seems to be of less importance than combustion particles in the development of allergic diseases after exposure to traffic-related air pollution.

Determinants of experimental allergic responses: interactions between allergen dose, sex and age

The prevalence of allergic diseases is influenced by sex and age. Although mouse models are widely used in allergy research, few experimental studies have examined the interaction effects of sex and age on allergy outcomes. Our aim was to investigate the individual and combined effects of sex and age on allergic sensitization and inflammation in two mouse models: an intraperitoneal (i.p.) and an intranasal (i.n.) sensitization model. We also investigated how the allergen immunization dose interacted with age and sex in the i.p. model. Female and male mice were immunized i.p. or i.n. with ovalbumin when 1, 6 or 20 weeks old. In both models, allergen challenges were performed by i.n. delivery. Serum antibodies, draining lymph node cytokine release and airway inflammatory responses were assessed. In the i.p. model, the antibody and cytokine levels and airway inflammation were highly influenced by immunization dose and age. The responses increased with age when using a low immunization dose, but decreased with age when using a high immunization dose. In the i.n. model, antibody production and airway tissue inflammation increased with age. Female compared with male mice generally developed more pronounced antibody and inflammatory responses. Relative to older mice, juvenile mice had augmented airway inflammation to allergen exposures. The study demonstrates that immunization dose, sex and age are highly influential on allergy outcomes. To better mimic different life stages of human allergic airway disease, murine models, therefore, require careful optimization.

Prediction of fluid velocity slip at solid surfaces

The observed flow enhancement in highly confining geometries is believed to be caused by fluid velocity slip at the solid wall surface. Here we present a simple and highly accurate method to predict this slip using equilibrium molecular dynamics. Unlike previous equilibrium molecular dynamics methods, it allows us to directly compute the intrinsic wall-fluid friction coefficient rather than an empirical friction coefficient that includes all sources of friction for planar shear flow. The slip length predicted by our method is in excellent agreement with the slip length obtained from direct nonequilibrium molecular dynamics simulations.

Structure and stability of the spinach aquaporin SoPIP2;1 in detergent micelles and lipid membranes

Background

SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1.

Methodology/Principal Finding

We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C.

Conclusion/Significance

The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications.

Assessing the efficacy of vesicle fusion with planar membrane arrays using a mitochondrial porin as reporter

Reconstitution of functionally active membrane protein into artificially made lipid bilayers is a challenge that must be overcome to create a membrane-based biomimetic sensor and separation device. In this study we address the efficacy of proteoliposome fusion with planar membrane arrays. We establish a protein incorporation efficacy assay using the major non-specific porin of Fusobacterium nucleatum (FomA) as reporter. We use electrical conductance measurements and fluorescence microscopy to characterize proteoliposome fusion with an array of planar membranes. We show that protein reconstitution in biomimetic membrane arrays may be quantified using the developed FomA assay. Specifically, we show that FomA vesicles are inherently fusigenic. Optimal FomA incorporation is obtained with a proteoliposome lipid-to-protein molar ratio (LPR)=50 more than 10(5) FomA proteins could be incorporated in a bilayer array with a total membrane area of 2mm(2) within 20 min. This novel assay for quantifying protein delivery into lipid bilayers may be a useful tool in developing biomimetic membrane applications.

Viscosity kernel of molecular fluids: butane and polymer melts

The wave-vector dependent shear viscosities for butane and freely jointed chains have been determined. The transverse momentum density and stress autocorrelation functions have been determined by equilibrium molecular dynamics in both atomic and molecular hydrodynamic formalisms. The density, temperature, and chain length dependencies of the reciprocal and real-space viscosity kernels are presented. We find that the density has a major effect on the shape of the kernel. The temperature range and chain lengths considered here have by contrast less impact on the overall normalized shape. Functional forms that fit the wave-vector-dependent kernel data over a large density and wave-vector range have also been tested. Finally, a structural normalization of the kernels in physical space is considered. Overall, the real-space viscosity kernel has a width of roughly 3-6 atomic diameters, which means that generalized hydrodynamics must be applied in predicting the flow properties of molecular fluids on length scales where the strain rate varies sufficiently in the order of these dimensions (e.g., nanofluidic flows).

An extended analysis of the viscosity kernel for monatomic and diatomic fluids

We present an extended analysis of the wavevector dependent shear viscosity of monatomic and diatomic (liquid chlorine) fluids over a wide range of wavevectors and for a variety of state points. The analysis is based on equilibrium molecular dynamics simulations, which involve the evaluation of transverse momentum density and shear stress autocorrelation functions. For liquid chlorine we present the results in both atomic and molecular formalisms. We find that the viscosity kernel of chlorine in the atomic representation is statistically indistinguishable from that in the molecular representation. The results further suggest that the real space viscosity kernels of monatomic and diatomic fluids depend sensitively on the density, the potential energy function and the choice of fitting function in reciprocal space. It is also shown that the reciprocal space shear viscosity data can be fitted to two different simple functional forms over the entire density, temperature and wavevector range: a function composed of n-Gaussian terms and a Lorentzian-type function. Overall, the real space viscosity kernel has a width of 3-6 atomic diameters, which means that the generalized hydrodynamic constitutive relation is required for fluids with strain rates that vary nonlinearly over distances of the order of atomic dimensions.