Monomer Size Research Articles

N-Linked Glycosylation Regulates CALHM1 Channel Function and Subcellular Localization

Calcium homeostasis modulator 1 (CALHM1) was discovered as a susceptibility gene for late-onset Alzheimer's disease. CALHM1 has been established as a pore-forming subunit of a homohexameric voltage-gated, non-selective ion channel and its important physiological roles including neuronal excitability and taste perception have also been revealed. However, other modes of CALHM1 channel regulation including ones mediated by post-translational modifications remain to be elucidated. On a western blot, heterologously expressed mouse CALHM1 (mCALHM1) immunosignal appears as three bands with one band at the size of a mCALHM1 monomer, approximately 37 kDa, and the other two bands at higher molecular weights, suggesting post-translational modifications on CALHM1. The two higher molecular weight bands disppeared after peptide-N-glycosidase F treatment, demonstrating that mCALHM1 is glycosylated at asparagine (N) residue(s). Point mutation studies determined that a conserved N139 is the only N-glycosylation site on mCALHM1. The two glycosylated forms of mCALHM1 showed different sinsitivities to endoglycosidase H, demonstrating that conversion of the acquired N-linked glycan chain from high-mannose type to complex type takes place. Furthermore, by using chemical and enzymatic reagents, point mutation studies, and glycosylation mutant cell lines, we examined roles of acquisition and conversion of the N-linked glycan on function and subcellular localization of mCALHM1 channel. Our data provide insights into a novel regulation of CALHM1 channel by N-linked glycosylation.

Effects of molecular crowding and confinement on the spatial organization of a biopolymer.

A chain molecule can be entropically collapsed in a crowded medium in a free or confined space. Here, we present a unified view of how molecular crowding collapses a flexible polymer in three distinct spaces: free, cylindrical, and (two-dimensional) slit-like. Despite their seeming disparities, a few general features characterize all these cases, even though the ϕc-dependence of chain compaction differs between the two cases: a > ac and a < ac, where ϕc is the volume fraction of crowders, a is the monomer size, and ac is the crowder size. For a > ac (applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio aϕc/ac, and "full" compaction occurs universally at aϕc/ac ≈ 1; for ac > a (relevant for protein folding), it is controlled by ϕc alone and crowding has a modest effect on chain size in a cellular environment (ϕc ≈ 0.3). Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independent of confinement.

Photopolymerization Kinetics of Different Chain Sizes of Bi-functional Acrylic Monomers using Real Time FT-IR

Photopolymerization Kinetics of Different Chain Sizes of Bi-functional Acrylic Monomers using Real Time FT-IR

Catalysis of Silver catfish Major Hepatic Glutathione Transferase proceeds via rapid equilibrium sequential random Mechanism

Fish hepatic glutathione transferases are connected with the elimination of intracellular pollutants and detoxification of organic micro-pollutants in their aquatic ecosystem. The two-substrate steady state kinetic mechanism of Silver catfish (Synodontis eupterus) major hepatic glutathione transferases purified to apparent homogeneity was explored. The enzyme was dimeric enzyme with a monomeric size of 25.6 kDa. Initial-velocity studies and Product inhibition patterns by methyl glutathione and chloride with respect to GSH-CDNB; GSH-ρ-nitrophenylacetate; and GSH-Ethacrynic acid all conforms to a rapid equilibrium sequential random Bi Bi kinetic mechanism rather than steady state sequential random Bi Bi kinetic. α was 2.96 ± 0.35 for the model. The pH profile of Vmax/KM (with saturating 1-chloro-2,4-dinitrobenzene and variable GSH concentrations) showed apparent pKa value of 6.88 and 9.86. Inhibition studies as a function of inhibitor concentration show that the enzyme is a homodimer and near neutral GST. The enzyme poorly conjugates 4-hydroxylnonenal and cumene hydroperoxide and may not be involved in oxidative stress protection. The seGST is unique and overwhelmingly shows characteristics similar to those of homodimeric class Pi GSTs, as was indicated by its kinetic mechanism, substrate specificity and inhibition studies. The rate- limiting step, probably the product release, of the reaction is viscosity-dependent and is consequential if macro-viscosogen or micro-viscosogen.

Soot aggregate complex morphology: 3D geometry reconstruction by SEM tomography applied on soot issued from propane combustion

Characterization of soot is of interest to many researchers working on environmental aerosol and combustion diagnostics over decades. In this study the morphology of soot aggregates issued from incomplete combustion is investigated based on the need of their radiative properties. The state-of-art of the work on soot from incomplete combustions comprises the characterization techniques based on in situ and ex situ techniques. Due to the limitations and uncertainties arising from in situ measurements in a combustion flame for the definition of morphology for a dispersed group of aggregates, ex situ observations under electron microscopy are often referred to in the literature for aggregate samples collected inside the flame. The latter ex situ observations include the fractal analysis of 2D SEM/TEM images, the derivation of 3D geometry obtained by TEM tomography and the generation of numerical aggregates based on common fractal parameters. In our study, soot aggregates are extracted from a laboratory scale rich propane-air flame by thermophoretic sampling onto metal thin plates. Different from the previous researches, 3D geometry of soot is obtained here by SEM tomography: the geometry reconstruction techniques are successfully applied to a relatively small series of tilted SEM images of high resolution using the “seeing through” phenomenon occurring in nano-sized material samples with low atomic number. The observation of soot monomer size under TEM microscopy allows us to test the errors that may arise from the SEM imaging technique (like the pollution deposition on the substrate due to charging, the image artifacts due to the nature of secondary electron emissions) and from the simplified sampling procedure (not using the conventional holey carbon films but metal thin plates). The obtained 3D soot geometry is promising in terms of reducing the analysis time, simplifying the sampling procedure and expanding the 3D observation applicability by not limiting the material sampling to depositing soot and aerosols on TEM grids.

Sensitivity analysis of aggregate morphology on mass-mobility relationship and improved parameterizations

AbstractPast studies have shown that the diffusion-limited cluster aggregation mechanism yields aggregates with a mass fractal dimension (Df) of around 1.8 and power-law prefactor (kf) ranging between 1.2 and 2.5. For a fixed Df, an increasing kf physically manifests as decreasing shape anisotropy or the degree of “stringiness” of an aggregate. In this work, we investigate the effects of changing kf, monomer size (d), and number of monomers (N) of computer-simulated aggregates on their mass-mobility scaling exponent (Dfm) and prefactor (kfm). Our simulation results for a statistically significant number of Df = 1.78 ± 0.10 aggregates yielded Dfm values of 2.20 ± 0.05. These values are in excellent agreement with previous experimental observations. While variations in Dfm were predominantly influenced by Df, kfm showed sensitivity to fluctuations in kf. The validity and accuracy of the empirical power-law exponent 1.08 used for estimating N in three dimensions from two dimensional projection images was als...

Synthesis of Titanium Dioxide Aerosol Gels in a Buoyancy-Opposed Flame Reactor

Aerosol gels are a novel class of materials with potential to serve in various energy and environmental applications. In this work, we demonstrate the synthesis of titanium dioxide (TiO2) aerosol gels using a methane-oxygen coflow diffusion flame reactor operated in down-fired configuration (fuel flow in the direction opposite to buoyancy forces). Titanium tetraisopropoxide was fed as a precursor to the flame under different operating conditions. Control of the monomer size and crystalline phase of TiO2 gel particles was achieved by adjusting the flame operating conditions, specifically the flame temperature, which was shown to significantly influence the phase transformation and rate of particle growth and sintering. The resulting materials were characterized for their physical and optical properties. Results showed that the TiO2 aerosol gels had effective densities in the range 0.021–0.025 g/cm3, which is 2 orders of magnitude less than the theoretical mass density of TiO2. The monomer size distribution, crystalline phase, and UV-Vis absorbance spectra of the gels showed distinct characteristics as a function of flame temperature.Copyright © 2015 American Association for Aerosol Research

Irreversible Adsorption of Worm-Like Chains

We present a theory for the irreversible adsorption of semiflexible polymers, described as worm-like chains (WLC) of persistence length l and contour length S, from dilute solution, with a focus on chemisorption (reaction limited adsorption). Early stages are dominated by single chain adsorption. For stiff to moderately flexible chains, shorter than S*∼ l5/3/b2/3 with b the monomer size, adsorption proceeds out of the first binding point with minimal, flat, adsorption loops of size so ∼ l1/3 b2/3 by simple zipping in S/s0 steps. For more flexible chains obeying S > S*, adsorption proceeds by multiple zipping from several nucleation points distant along the chain. At a certain typical surface concentration, larger than the 2-d overlap concentration, steric hindrance between incoming polymers and those lying already flat on the surface becomes relevant. The interfacial profile built by stiff loops dangling in the solution comprises an inner layer and an outer layer, where the concentration decreases with th...

Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes.

Protocols that aim to construct complete models of multiprotein complexes based on ion mobility and mass spectrometry data are becoming an important element of integrative structural biology efforts. However, the usefulness of such data is predicated, in part, on an ability to measure individual subunits removed from the complex while maintaining a compact/folded state. Gas-phase dissociation of intact complexes using collision induced dissociation is a potentially promising pathway for acquiring such protein monomer size information, but most product ions produced are possessed of high charge states and elongated/string-like conformations that are not useful in protein complex modeling. It has previously been demonstrated that the collision induced dissociation of charge-reduced protein complexes can produce compact subunit product ions; however, their formation mechanism is not well understood. Here, we present new experimental evidence for the avidin (64 kDa) and aldolase (157 kDa) tetramers that demonstrates significant complex remodeling during the dissociation of charge-reduced assemblies. Detailed analysis and modeling indicates that highly compact intermediates are accessed during the dissociation process by both complexes. Here, we present putative pathways that describe the formation of such ions, as well as discuss the broader significance of such data for structural biology applications moving forward.

Solvent Effects on Acrylate kp in Organic Media: A Response.

Radical propagation rate is adequately understood in the light of fundamental kinetic theory. Differences in bulk and solution k(p) are primarily of entropic origin, with the effects depending on the differences in polarity and size of monomer and solvent molecules, respectively. Experimental data for the propagation rate coefficient of secondary acrylate radicals demonstrate that bulk and solution-in-toluene k(p) exhibit distinctly different behavior. Bulk k(p) is clearly enhanced in passing from methyl acrylate (MA) to dodecyl acrylate (DA), whereas solution-in-toluene k(p) is approximately constant with a slight tendency to decrease from MA to DA. This kp behavior has also been found in a recent study, in which it has, however, been concluded that k(p) in solution of toluene (and of butyl acetate) displays a similar behavior to bulk. This surprising and ina-dequate conclusion requires the present comment and rectification to be made.

The Effects of Monomer Size Distribution on the Radiative Properties of Black Carbon Aggregates

Black carbon (BC), normally existing as aggregates, significantly affects the Earth radiative forcing, energy balance, and climate by scattering and absorbing both solar radiation and terrestrial emission. The BC particles are usually treated as fractal aggregates with same-sized monomers. However, experimental studies show that monomer diameters of BC normally obey a lognormal distribution ranging from 10 nm to over 100 nm. This study investigates the effects of monomer size distribution on the radiative properties of BC particles. The fractal aggregates are generated by a cluster–cluster aggregation (CCA) algorithm, and the Multiple Sphere T-Matrix (MSTM) method is used to simulate the radiative properties of randomly oriented aggregates. The integral radiative properties of aggregates with different-sized monomers have normal distributions with large standard deviations, and it requires to average radiative properties of over 60 aggregate realizations to represent their ensemble-averaged properties. Th...

Polydisperse Size Distribution of Monomers and Aggregates of Sulfur-Containing Compounds in Petroleum Residue Fractions

Dimension of sulfur-containing compounds in a residue is crucial to hydrodesulfurization catalyst design. Size distributions of sulfur compounds in fractions of Venezuela atmospheric residue were determined from the bulk-phase diffusion coefficients, which were measured at 298 K by a diaphragm cell by using 200 nm polycarbonate membranes. Sulfur compounds in all fractions show obvious size polydispersity. The size of four narrow SFEF (supercritical fluid extraction and fraction) fractions varies slightly with the concentrations of 1 g/L to 40 g/L. However, maltenes and asphaltenes from the end-cut showed significant variation in size over concentrations of 0.1 g/L to 40 g/L, which indicates a coexistence of various monomers and aggregates. The monomers are dominated in maltenes, whereas aggregates dominated in asphaltenes. The hydrodynamic diameter of sulfur-containing monomers of four SFEF fractions ranges from 0.74 to 1.45 nm at a concentration of 1 g/L. The size of maltene monomers spans a range of 1.8...

Understanding of Relaxor Ferroelectric Behavior of Poly(vinylidene fluoride–trifluoroethylene–chlorotrifluoroethylene) Terpolymers

Relaxor ferroelectric poly(vinylidene fluoride) (PVDF) based terpolymers are attracting tremendous interest because of their potential applications in advanced energy harvesting and storage devices. Fundamental understanding of the ferroelectric behaviors of poly(vinylidene fluoride) (PVDF) based terpolymers has proved elusive. Current research suggests that the existence of different hysteresis loops results from physical pinning of the ferroelectric domains by the bulky defect monomers and that the size of the defect monomer determines the ferroelectric behavior. In this study, a poly(vinylidene fluoride-ter-trifluoroethylene-ter-chlorotrifluoroethylene) random terpolymer is processed using a variety of methods and found to exhibit normal ferroelectric, single hysteresis loop (SHL), and double hysteresis loop (DHL) behaviors depending on the processing method. This indicates that the ferroelectric behavior of the terpolymer is related to not only the size of an individual defect unit but also how they are arranged within the relaxor ferroelectric phase. The results show that DHL behavior is a result of paraelectric domains that are promoted by long crystallization times, while the SHL behavior stems from a more random dispersion of these defects.

Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex.

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.

Reformulation of charge transfer and material balance equations of polaron-containing polymer films

As known, polaron quasi-particles of conducting polymers contain from 3 to 6 monomer fragments (repeat units) of polymer chains. This is the reason why the widely accepted approach to treating the polaron conductance assumes that the reduced forms of polarons have the same number of repeat units as included into polarons and, moreover, treats such reduced formations as separate quasi-particles. The latter obviously means that charge transfer from a polaron to a neighboring reduced quasi-particle proceeds with simultaneous transformations of all the fragments of these quasi-particles. In other words, the distance of charge transfer in such transitions is assumed to be exactly equal to the polaron size. In contrast to such treatment, the main feature of the proposed approach is a polaron flux reformulation, which assumes a unit polaron translocation to be of a one monomer size independently of number m of monomer fragments included into polaron quasi-particles. As a result, material balance equations of polaron-conducting films take a more complicated form than that accepted in the existing approach. It is shown that, at equilibrium conditions, the obtained equations, as it must be, lead to the relationships being in accordance with thermodynamic ones. At the same time, a proper analysis reveals some differences between quantitative results that follow from the proposed and traditional approaches for both quasi-equilibrium and non-equilibrium conditions. Possible directions of the further development of the represented approach are shortly discussed.

OUTWARD MOTION OF POROUS DUST AGGREGATES BY STELLAR RADIATION PRESSURE IN PROTOPLANETARY DISKS

We study the dust motion at the surface layer of protoplanetary disks. Dust grains in surface layer migrate outward due to angular momentum transport via gas-drag force induced by the stellar radiation pressure. In this study, we calculate mass flux of the outward motion of compact grains and porous dust aggregates by the radiation pressure. The radiation pressure force for porous dust aggregates is calculated using the T-Matrix Method for the Clusters of Spheres. First, we confirm that porous dust aggregates are forced by strong radiation pressure even if they grow to be larger aggregates in contrast to homogeneous and spherical compact grains to which efficiency of radiation pressure becomes lower when their sizes increase. In addition, we find that the outward mass flux of porous dust aggregates with monomer size of 0.1 $\mu$m is larger than that of compact grains by an order of magnitude at the disk radius of 1 AU, when their sizes are several microns. This implies that large compact grains like calcium-aluminum rich inclusions (CAIs) are hardly transported to outer region by stellar radiation pressure, whereas porous dust aggregates like chondritic-porous interplanetary dust particles (CP-IDPs) are efficiently transported to comet formation region. Crystalline silicates are possibly transported in porous dust aggregates by stellar radiation pressure from inner hot region to outer cold cometary region in the protosolar nebula.

Exploring the glass transition region: crowding effect, nonergodicity and thermorheological complexity

Monte Carlo simulations performed on multiple polymer chains have produced accurate relaxation modulus Gs(t) curves which match the experimental G(t) curves of polystyrene reasonably well, over a wide temperature range around the glass transition region. The inter-segmental interactions, defined in terms of ε* (well depth) and σ (monomer size), exert a strong influence on the modulus, the length scale and the relaxation time scale of the system. Judicious selection of these interaction parameters has enabled us to create the whole range of temperature dependence of the thermorheological complexity, from ΔT = 40 °C to ΔT = 0 °C. Near the glass transition temperature, the development of nonergodicity vis-à-vis a crowding effect in the system emerges naturally from the analysis of the G(t) line shapes. The entropic slow mode is well described by the Rouse theory and the energetic fast mode shifts to longer time scales, revealing the generic behavior of the thermorheological complexity. Typical Gs(t) curves, when partitioned into glassy and rubbery components, are shown to obey Inoue-Okamoto-Osaki's modified stress-optical rule, with different stress-optical coefficients for each component. Closer to the glass transition temperature, the distance of the closest monomer shows a considerable increase, suggesting a penetrable resistance to the approach of another monomer. The parameter σ represents the characteristic length scale of the system in the glassy region. The thermorheological complexity incorporates the dynamic length scale of structural relaxation, increasing with the decrease of temperature towards the glass transition point.

Semiflexible polymer brushes and the brush-mushroom crossover.

Semiflexible polymers end-grafted to a repulsive planar substrate under good solvent conditions are studied by scaling arguments, computer simulations, and self-consistent field theory. Varying the chain length N, persistence length lp, and grafting density σg, the chain linear dimensions and distribution functions of all monomers and of the free chain ends are studied. Particular attention is paid to the limit of very small σg, where the grafted chains behave as "mushrooms" no longer interacting with each other. Unlike a flexible mushroom, which has a self-similar structure from the size (a) of an effective monomer up to the mushroom height (h/a ∝ N(v), ν ≈ 3/5), a semiflexible mushroom (like a free semiflexible chain) exhibits three different scaling regimes, h/a ∝ N for contour length L = Na < lp, a Gaussian regime, h/a ∝ (Llp)(1/2)/a for lp ≪ L ≪ R* ∝ (lp(2)/a), and a regime controlled by excluded volume, h/a ∝ (lp/a)(1/5)N(ν). The semiflexible brush is predicted to scale as h/a ∝ (lpaσg)(1/3)N in the excluded volume regime, and h/a ∝ (lpa(3)σ(2))(1/4)N in the Gaussian regime. Since in the volume taken by a semiflexible mushroom excluded-volume interactions are much weaker in comparison to a flexible mushroom, there occurs an additional regime where semiflexible mushrooms overlap without significant chain stretching. Moreover, since the size of a semiflexible mushroom is much larger than the size of a flexible mushroom with the same N, the crossover from mushroom to brush behavior is predicted to take place at much smaller densities than for fully flexible chains. The numerical results, however, confirm the scaling predictions only qualitatively; for chain lengths that are relevant for experiments, often intermediate effective exponents are observed due to extended crossovers.

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide.

The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.

Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum.

Tandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here, we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.