Ultrastructure of feeding in the karyorelictean ciliate Tracheloraphis examined by scanning electron microscopy

The karyorelictean ciliate Tracheloraphis is considered to be among the most primitive of the extant ciliates based on both nuclear and somatic characters. These organisms lack the elaborate oral ciliation present in most ciliates. Their mode of ingestion is a type of phagocytosis through a non-ciliated region, the glabrous stripe, which runs the length of the cell. This type of ingestion is reminiscent of feeding in amoebae and some flagellate groups. It is possible that ciliate oral structures evolved within the karyorelictean ciliates from an ancestor resembling Tracheloraphis. We studied the ingestion process in a Tracheloraphis species from the Chesapeake Bay using scanning electron microscopy. The results indicate that the anterior terminus of the organism is not involved in the actual ingestion process, only the glabrous stripe. There is some interaction between the food particle and the surface of the stripe, possibly mediated by a substance secreted by the underlying extrusomes. The somatic cilia do not appear to be involved. The stripe invaginates at the ingestion site engulfing the particle. The cell becomes greatly distended at this site, but neither the anterior nor posterior terminus is affected.     

Role of streams in myxobacteria aggregate formation

Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.     

Key structural features of the actin filament Arp2/3 complex branch junction revealed by molecular simulation

We investigated the structure, properties and dynamics of the actin filament branch junction formed by actin-related protein (Arp) 2/3 complex using all-atom molecular dynamics (MD) simulations based on a model fit to a reconstruction from electron tomograms. Simulations of the entire structure consisting of 31 protein subunits together with solvent molecules containing ～3 million atoms were performed for an aggregate time of 175 ns. One 75-ns simulation of the original reconstruction was compared to two 50-ns simulations of alternate structures, showing that the hypothesized branch junction structure is very stable. Our simulations revealed that the interface between Arp2/3 complex and the mother actin filament features a large number of salt bridges and hydrophobic contacts, many of which are dynamic and formed/broken on the timescale of the simulation. The simulations suggest that the DNase binding loops in Arp3, and possibly Arp2, form stabilizing contacts with the mother filament. Unbiased comparison of models sampled from the MD simulation trajectory with the primary experimental electron tomography data identified regions were snapshots from the simulation provide atomic details of the model structures and also pinpoints regions where the initial modeling based on the electron tomogram reconstruction may be suboptimal.     

Organ printing: fiction or science

Aggregates of living cells (i.e. model tissue fragments) under appropriate conditions fuse like liquid drops. According to Steinberg's differential adhesion hypothesis (DAH), this may be understood by assuming that cells are motile and tissues made of such cells possess an effective surface tension. Here we show that based on these properties three-dimensional cellular structures of prescribed shape can be constructed by a novel method: cell aggregate printing. Spherical aggregates of similar size made of cells with known adhesive properties were prepared. Aggregates were embedded into biocompatible gels. When the cellular and gel properties, as well as the symmetry of the initial configuration were appropriately adjusted the contiguous aggregates fused into ring-like organ structures. To elucidate the driving force and optimal conditions for this pattern formation, Monte Carlo simulations based on a DAH motivated model were performed. The simulations reproduced the experimentally observed cellular arrangements and revealed that the control parameter of pattern evolution is the gel-tissue interfacial tension, an experimentally accessible parameter.     

Engineering amyloidogenicity towards the development of nanofibrillar materials

When folded into their native structures, proteins in biological systems function as nanostructured machines. By contrast, some polypeptides tend to aggregate into other well-ordered structures, namely amyloid fibrils. Such well-ordered protein fibrils are attractive materials for nanobiotechnology because they self-associate through noncovalent bonds under controlled conditions - a property that is shared with small organic molecules called organogelators. Recently, the use of amyloid fibrils as structural templates for constructing nanowires has been demonstrated. Such applications will potentially become one of the next trends in protein engineering and nanobiotechnology.     

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs.     

A local activator-inhibitor model of vertebrate skin patterns

A model for vertebrate skin patterns is presented in which the differentiated (colored) pigment cells produce two diffusible morphogens, an activator and an inhibitor. The concentrations of these two substances at any point on the skin determine whether a pigment cell at that point will be colored or not. Computer simulations with this model show many realistic features of spot and stripe patterns found in vertebrates.     

Melanophores in the stripes of adult zebrafish do not have the nature to gather,but disperse when they have the space to move

Animal skin pattern is one of the good model systems used to study the mechanism of pattern formation. Molecular genetic studies with zebrafish have shown that pigment cells play a major role in the mechanism of stripe formation. Among the variety of cellular events that may be involved in the mechanism, aggregation of melanophores has been suggested as an important factor for pattern formation. However, only a few experimental studies detected the migration ability of melanophores in vivo. Here, we tried to determine whether melanophores really have the ability to aggregate in the skin of zebrafish. Melanophores in the adult stripes are packed densely and they rarely move. However, when the neighboring pigment cells are killed, they move and regenerate the stripe pattern, suggesting that melanophores retain the migration ability. To analyze the migration, we ablated a part of the melanophores by laser to give free space to the remaining cells; we then traced the migration. Contrary to our expectation, we found that melanophores repulsed one another and dispersed from the aggregated condition in the absence of xanthophores. Apparent aggregation may be forced by the stronger repulsive effect against the xanthophores, which excludes melanophores from the yellow stripe region.     

Brownian Dynamics Computer Simulations of Quenched Lennard-Jones-like Fluids: I Morphology and Local Structural Evolution

Abstract

The structural characteristics during phase separation of a model colloidal system were investigated using Brownian dynamics simulation. The structures that formed were analysed using the radial distribution function and structure factor in separate time periods after the quench. The data were interpreted in terms of scale-invariancy and density inhomogeneities. The systems, which consisted of a gas-like phase and dense liquid or solid-like regions, developed with a highly interconnected morphology during the simulations. The aggregate morphology was sensitive to the range of the attractive part of the potential and the position in the phase diagram after the quench. The long-range 12:6 potential induced compact structures with thick filaments, whereas the systems generated using the shorter-ranged 24:12 and 36:18 potentials persisted in a more diffuse network and also evolved more slowly with time. The fractal dimensions were quite high, typically close to 3. The 24:12 and 36:18 potential systems developed regions of local crystalline order which formed contemporaneously with the more global morphological changes. In contrast, at low temperatures the particles of the longer-range 12:6 potential became trapped in glass-like states during the course of the morphological changes in the system. The value of the characteristic lengthscale with time exponent, α, was found to be dependent on the temperature, density and interaction potential and therefore cannot be described as ‘universal’.     

Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics

Five long-timescale (10 ns) explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide dimer are performed using the GROMOS 45A4 force field and the simple-point-charge water model, in order to investigate the effect of the treatment of long-range electrostatic interactions as well as of the box shape and size on the structure and dynamics of the molecule (starting from an idealised B-DNA conformation). Long-range electrostatic interactions are handled using either a lattice-sum (LS) method (particle–particle–particle–mesh; one simulation performed within a cubic box) or a cutoff-based reaction-field (RF) method (four simulations, with long-range cutoff distances of 1.4 or 2.0 nm and performed within cubic or truncated octahedral periodic boxes). The overall double-helical structure, including Watson–Crick (WC) base-pairing, is well conserved in the simulation employing the LS scheme. In contrast, the WC base-pairing is nearly completely disrupted in the four simulations employing the RF scheme. These four simulations result in highly distorted compact (cutoff distance of 1.4 nm) or extended (cutoff distance of 2 nm) structures, irrespective of the shape and size of the computational box. These differences observed between the two schemes seem correlated with large differences in the radial distribution function between charged entities (backbone phosphate groups and sodium counterions) within the system.     

Polyelectrolyte precipitation of proteins: II. Models of the particle size distributions

A population-balance model has been used to characterize continuous polyelectrolyte precipitation of egg white proteins. We have modeled the particle size distributions of aggregates formed under a range of mixing conditions. The models, accounting for aggregate growth (by both shear-driven and Brownian-like collisions), breakage (by hydrodynamic shear or aggregate-aggregate collisions), and birth (by the breakage of large aggregates), fit the data well. The kinetic constants show dependencies on shear rate and residence time that have not been previously theoretically predicted; these dependencies are due in part to aging effects on the aggregate. The model constants show a dominance of growth over breakage, supporting qualitative interpretations of the particle size distributions. A mechanism for growth-rate enhancement, caused by polymer extensions from the particle surfaces, produced improved model performance. A collisional breakage mechanism is supported.     

Aggregation of small peptides studied by molecular dynamics simulations

Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer's disease, type II diabetes, and various prion diseases. Lately, it has been observed that even very short peptides like tetra and pentapeptides can form ordered amyloid structures. Here, we present aggregation studies of three such small polypeptide systems, namely, the two amyloidogenic peptides DFNKF and FF, and a control (nonamyloidogenic) one, the AGAIL. The respective aggregation process is studied by all-atom Molecular Dynamics simulations, which allow to shed light on the fine details of the association and aggregation process. Our analysis suggests that naturally aggregating systems exhibit significantly diverse overall cluster shape properties and specific intermolecular interactions. Additional analysis was also performed on the previously studied NFGAIL system.     

Protein surface roughness accounts for binding free energy of Plasmepsin II‐ligand complexes

The calculation of absolute binding affinities for protein‐inhibitor complexes remains as one of the main challenges in computational structure‐based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high‐resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x‐ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave‐one‐out cross‐validation showed that our model reproduced accurately the absolute binding free energies for our training set (R² = 0.76; <|error|> =0.55 kcal/mol; SD_error = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article.     

Structures of Discoidal High Density Lipoproteins: A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH*

Conversion of discoidal phospholipid (PL)-rich high density lipoprotein (HDL) to spheroidal cholesteryl ester-rich HDL is a central step in reverse cholesterol transport. A detailed understanding of this process and the atheroprotective role of apolipoprotein A-I (apoA-I) requires knowledge of the structure and dynamics of these various particles. This study, combining computation with experimentation, illuminates structural features of apoA-I allowing it to incorporate varying amounts of PL. Molecular dynamics simulated annealing of PL-rich HDL models containing unesterified cholesterol results in double belt structures with the same general saddle-shaped conformation of both our previous molecular dynamics simulations at 310 K and the x-ray structure of lipid-free apoA-I. Conversion from a discoidal to a saddle-shaped particle involves loss of helicity and formation of loops in opposing antiparallel parts of the double belt. During surface expansion caused by the temperature-jump step, the curved palmitoyloleoylphosphatidylcholine bilayer surfaces approach planarity. Relaxation back into saddle-shaped structures after cool down and equilibration further supports the saddle-shaped particle model. Our kinetic analyses of reconstituted particles demonstrate that PL-rich particles exist in discrete sizes corresponding to local energetic minima. Agreement of experimental and computational determinations of particle size/shape and apoA-I helicity provide additional support for the saddle-shaped particle model. Truncation experiments combined with simulations suggest that the N-terminal proline-rich domain of apoA-I influences the stability of PL-rich HDL particles. We propose that apoA-I incorporates increasing PL in the form of minimal surface bilayers through the incremental unwinding of an initially twisted saddle-shaped apoA-I double belt structure.     

Simulations of kinetically irreversible protein aggregate structure.

We have simulated the structure of kinetically irreversible protein aggregates in two-dimensional space using a lattice-based Monte-Carlo routine. Our model specifically accounts for the intermolecular interactions between hydrophobic and hydrophilic protein surfaces and a polar solvent. The simulations provide information about the aggregate density, the types of inter-monomer contacts and solvent content within the aggregates, the type and extent of solvent exposed perimeter, and the short- and long-range order all as a function of (i) the extent of monomer hydrophobic surface area and its distribution on the model protein surface and (ii) the magnitude of the hydrophobic-hydrophobic contact energy. An increase in the extent of monomer hydrophobic surface area resulted in increased aggregate densities with concomitant decreased system free energies. These effects are accompanied by increases in the number of hydrophobic-hydrophobic contacts and decreases in the solvent-exposed hydrophobic surface area of the aggregates. Grouping monomer hydrophobic surfaces in a single contiguous stretch resulted in lower aggregate densities and lower short range order. More favorable hydrophobic-hydrophobic contact energies produced structures with higher densities but the number of unfavorable protein-protein contacts was also observed to increase; greater configurational entropy produced the opposite effect. Properties predicted by our model are in good qualitative agreement with available experimental observations.     

Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations

The pathological manifestation of nine hereditary neurodegenerative diseases is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. To improve our understanding of the processes by which polyglutamine-containing proteins misfold and aggregate, we have conducted molecular dynamics simulations of the aggregation of model polyglutamine peptides. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms, depending on the residue being modeled. The effects of hydrophobicity on the system are studied by varying the strength of the hydrophobic interaction from 12.5% to 5% of the hydrogen-bonding interaction strength. In our simulations, we observe the spontaneous formation of aggregates and annular structures that are made up of beta-sheets starting from random configurations of random coils. This result was interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglutamine would form water-filled nanotubes.     

Interaction Between Amyloid-β (1-42) Peptide and Phospholipid Bilayers: A Molecular Dynamics Study

The amyloid-β (Aβ) peptide is a key aggregate species in Alzheimer's disease. Although important aspects of Aβ peptide aggregation are understood, the initial stage of aggregation from monomer to oligomer is still not clear. One potential mediator of this early aggregation process is interactions of Aβ with anionic cell membranes. We used unconstrained and umbrella sampling molecular dynamics simulations to investigate interactions between the 42-amino acid Aβ peptide and model bilayers of zwitterionic dipalmitoylphosphatidylcholine (DPPC) lipids and anionic dioleoylphosphatidylserine (DOPS) lipids. Using these methods, we determined that Aβ is attracted to the surface of DPPC and DOPS bilayers over the small length scales used in these simulations. We also found supporting evidence that the charge on both the bilayer surface and the peptide affects the free energy of binding of the peptide to the bilayer surface and the distribution of the peptide on the bilayer surface. Our work demonstrates that interactions between the Aβ peptide and lipid bilayer promotes a peptide distribution on the bilayer surface that is prone to peptide-peptide interactions, which can influence the propensity of Aβ to aggregate into higher-order structures.     

Optical Magnetic Resonances in Subwavelength Ag–MgF2–Ag Grating Structures

Optical magnetic responses were demonstrated in subwavelength Ag–MgF₂–Ag grating structures for transverse magnetic-polarized light. The subwavelength Ag–MgF₂–Ag grating structures were fabricated using e-beam lithography followed by a lift-off process. By fixing the Ag–MgF₂–Ag strip dimension, the effect of the stripe width on the magnetic resonances was compared for two different grating pitches. With further reduced grating pitch, we pushed the optical magnetic resonances to near UV (deep blue). Numerical simulations confirmed our experimental observations and were in good agreement with the experimental results.