Flexible Filaments Research Articles

The Saccharomyces cerevisiae Smc2/4 Condensin Compacts DNA into (+) Chiral Structures without Net Supercoiling

Smc2/4 forms the core of the Saccharomyces cerevisiae condensin, which promotes metaphase chromosome compaction. To understand how condensin manipulates DNA, we used two in vitro assays to study the role of SMC (structural maintenance of chromosome) proteins and ATP in reconfiguring the path of DNA. The first assay evaluated the topology of knots formed in the presence of topoisomerase II. Unexpectedly, both wild-type Smc2/4 and an ATPase mutant promoted (+) chiral knotting of nicked plasmids, revealing that ATP hydrolysis and the non-SMC condensins are not required to compact DNA chirally. The second assay measured Smc2/4-dependent changes in linking number (Lk). Smc2/4 did not induce (+) supercoiling, but instead induced broadening of topoisomer distributions in a cooperative manner without altering Lk(0). To explain chiral knotting in substrates devoid of chiral supercoiling, we propose that Smc2/4 directs chiral DNA compaction by constraining the duplex to retrace its own path. In this highly cooperative process, both (+) and (-) loops are sequestered (about one per kb), leaving net writhe and twist unchanged while broadening Lk. We have developed a quantitative theory to account for these results. Additionally, we have shown at higher molar stoichiometries that Smc2/4 prevents relaxation by topoisomerase I and nick closure by DNA ligase, indicating that Smc2/4 can saturate DNA. By electron microscopy of Smc2/4-DNA complexes, we observed primarily two protein-laden bound species: long flexible filaments and uniform rings or "doughnuts." Close packing of Smc2/4 on DNA explains the substrate protection we observed. Our results support the hypothesis that SMC proteins bind multiple DNA duplexes.

Viral Diversity in Hot Springs of Pozzuoli, Italy, and Characterization of a Unique Archaeal Virus, Acidianus Bottle-Shaped Virus, from a New Family, the Ampullaviridae

Virus-like particles with five different morphotypes were observed in an enriched environmental sample from a hot, acidic spring (87 to 93 degrees C, pH 1.5) in Pozzuoli, Italy. The morphotypes included rigid rods, flexible filaments, and novel, exceptional forms. Particles of each type were isolated, and they were shown to represent viable virions of five novel viruses which infect members of the hyperthermophilic archaeal genus Acidianus. One of these, named the Acidianus bottle-shaped virus, ABV, exhibits a previously unreported morphotype. The bottle-shaped virion carries an envelope which encases a funnel-shaped core. The pointed end of the virion is likely to be involved in adsorption and channeling of viral DNA into host cells. The broad end exhibits 20 (+/- 2) thin filaments which appear to be inserted into a disk, or ring, and are interconnected at their bases. These filaments are apparently not involved in adsorption. ABV virions contain six proteins in the size range 15 to 80 kDa and a 23.9-kb linear, double-stranded DNA genome. Virus replication does not cause lysis of host cells. On the basis of its unique morphotype and structure, we propose to assign ABV to a new viral family, the Ampullaviridae.

The rapid onset of elasticity during the assembly of the bacterial cell-division protein FtsZ

FtsZ, a prokaryotic homolog of eukaryotic tubulin, is a major constituent of the bacterial Z-ring, which contracts the cell wall during cell division. Because the mechanical properties of FtsZ are unknown, its function in the maintenance and constriction of the Z-ring is not well understood. Here, quantitative rheometry shows that, at physiological concentrations, FtsZ filaments form, extremely rapidly, highly elastic networks within physiological time scales (∼ minutes), much faster than other major dynamic cytoskeletal filaments, including microtubule, actin, and vimentin in eukaryotes. FtsZ networks display a relatively low viscosity and a high resilience against shear stresses, as well as an elasticity that depends weakly on concentration, G ∼ C 0.57, a power-law dependence consistent with crosslinked flexible filaments. Calcium, whose intracellular concentration increases during bacterial division, further enhances the elasticity of FtsZ networks through filament bundling, an effect that occurs in the presence of GTP, not GDP. These studies suggest that FtsZ filaments have the toughness to provide strong mechanical support for the maintenance and circumferential constriction of the bacterial Z-ring.

타이어의 벨트 부착력과 내구성능 간의 상관성 연구

A pneumatic tire is made up of many flexible filaments of high modulus cord of natural textile, synthetic polymer, glass fiber, or fine hard drawn steel embedded in and bonded to a matrix of low modulus polymetric material. Adhesion property of these materials is very important in tire durability safety because belt-leaving-belt tread separation reduces the ability of a driver to control a vehicle, whether or not the separation is accompanied by a loss of air. In this study adhesion test of carcass-belt-tread is conducted on material properties of 5 PCR tire model, which are on sale in domestic market and analyzed adhesion properties. For those tire models FMVSS 109 indoor high speed durability test is conducted to analyze the correlation between adhesion force and high speed performance of tires and found the correlation between the two test results.

Flow-induced vibrations of high mass ratio flexible filaments freely hanging in a flow

The behavior of high mass ratio flexible filaments freely hanging in steady horizontal uniform flows is experimentally and theoretically investigated. When the flow velocity is small, static equilibrium states, where the filaments are inclined to the flow, are observed. Then, above a critical value of the wind velocity, the filaments exhibit periodic oscillations in the vertical plane. The problem is theoretically addressed considering the beam theory equations for the filament dynamics where the action of the flowing fluid is modeled using semiempirical expressions. These equations are first solved for the stationary equilibrium states. Then, the stability of these steady solutions relative to small perturbations is analyzed. A good agreement between experimental and theoretical results is found.

Fluid-Structure Interaction Analysis of a Two-Dimensional Flag-in-Wind Problem by the ALE Finite Element Method

In a recent experiment, Zhang and co-workers found that a flexible filament in a flowing soap film can exhibit three states; stretched-straight, flapping, and bistability. When this experimental model is regarded as a one-dimensional flag in a two-dimensional fluid flow, their findings contradict the common idea that flags always flap in a wind. In this paper, the flag-in-wind problem is simulated by fluid-structure interaction finite element analysis where Navier-Stokes equations based on the ALE method are strongly coupled with Lagrangian equilibrium equations of the structure. In the simulation the three states are successfully reproduced, and the effects of some representative parameters on the amplitude and frequency of the oscillations are investigated to reveal the underlying mechanism involved in flag flapping.

Molecular dynamics simulation of the chain of magnetic particles and flexible filament model

Molecular dynamics simulation of the chain of magnetic particles and flexible filament model

Type IV pilus structure and bacterial pathogenicity.

Type IV pili are remarkably strong, flexible filaments with varied roles in bacterial pathogenicity. All Gram-negative bacterial surfaces have type IV pili, which are polymeric assemblies of the protein pilin that evoke the host immune response and are potential drug and vaccine targets. Pilin structures that have been solved using X-ray crystallography and nuclear magnetic resonance, together with models for pilus architectures inferred from electron microscopy, fibre diffraction and computation, have established a molecular basis for assembly and multi-functionality, with implications for therapeutic interventions.

Interaction between toothbrushes and toothpaste abrasive particles in simulated tooth cleaning

There are currently many toothbrush designs on the market incorporating different filament configurations such as filaments at various angles and different lengths and made from several different materials. In order to understand how the tooth cleaning process occurs there is a need to investigate in detail how the abrasive particles in a toothpaste interact with the filaments in a teeth cleaning contact and cause material removal from a plaque or stain layer. The following describes the development of optical apparatus to enable the visualisation of simulated teeth cleaning contacts. Studies have been carried out using the apparatus to investigate particle entrainment into the contact and how it differs with varying bristle configurations. The effects of filament stiffness and tip shape were also investigated. Various types of electric toothbrushes were also tested. The studies have shown how particles are trapped at the tips of toothbrush filaments. Particles, suspended in fluid, approach the filament tips, as they pass through they may become trapped. Greater particle entrainment into the filament tip contact occurs with a reciprocating action at low filament loads and deflections than with a sliding motion. Large particles are less likely to enter tip contacts and are trapped between tips or under the filament bend at higher loads. Whether the particles are likely to be trapped and how long they remain so depends on the filament stiffness and degree of splay on loading and the filament configuration. The direction the filaments point in, the number of filaments in a tuft, the spacing of the tufts and the way the filaments splay when deflected all have an influence on entrainment of particles. Tufts with tightly packed stiff filaments which deflected together on loading were more effective at trapping particles than more flexible filaments that splayed out on loading as they present more of a barrier to particle entry and exit from the tip region.

Core and Heterogeneity of β 2-Microglobulin Amyloid Fibrils as Revealed by H/D Exchange

Dialysis-related amyloidosis, which occurs in the patients receiving a long-term hemodialysis with high frequency, accompanies the deposition of amyloid fibrils composed of β 2-microglobulin (β2-m). In vitro, β2-m forms two kinds of fibrous structures at acidic pH. One is a rigid “mature fibril”, and the other is a flexible thin filament often called an “immature fibril”. In addition, a 22-residue peptide (K3 peptide) corresponding to Ser20 to Lys41 of intact β2-m forms rigid amyloid-like fibrils similar to mature fibrils. We compared the core of these three fibrils at single-residue resolution using a recently developed hydrogen/deuterium (H/D) exchange method with the dissolution of fibrils by dimethylsulfoxide (DMSO). The exchange time-course of these fibrils showed large deviations from a single exponential curve showing that, because of the supramolecular structures, the same residue exists in different environments from molecule to molecule, even in a single fibril. The exchange profiles revealed that the core of the immature fibril is restricted to a narrow region compared to that of the mature fibril. In contrast, all residues were protected from exchange in the K3 fibril, indicating that a whole region of the peptide is engaged in the β-sheet network. These results suggest the mechanism of amyloid fibril formation, in which the core β-sheet formed by a minimal sequence propagates to form a rigid and extensive β-sheet network.

Flexible magnetic filaments as micromechanical sensors.

We propose a new micromechanical approach to probe bending rigidity at molecular scale. Long flexible filaments made of magnetic colloids and linkers are shown to adopt under magnetic field a hairpin configuration. Measuring the hairpin curvature as a function of the field intensity and the linker length from diffracted light allows us to deduce the linker bending rigidity kappa. The technique is presented for two types of linkers: a spontaneously adsorbing polymer and a grafted biomolecular.

Coupled states of flapping flags

Experiments concerning the oscillatory motion of thin flexible filaments lying in flowing soap films have shown particularly interesting phenomena. For example, when two such “flapping” filaments were introduced to the flowing soap film the filaments oscillated in-phase (asymmetry) or in anti-phase (symmetry) depending only on their mutual separation. We have been able to numerically simulate these experiments and provide some additional data on how the interaction changes when the filament separation is varied. Our results show that the fundamental frequency is dominant (single mode) and that the oscillation consists of an asymmetric system for small separations. For larger separations of about one half of the filament length, the fundamental frequency is again dominant although the system exhibits symmetric motion in this case. However, the filaments appear to pass through a domain for which the oscillation is possibly quasi-periodic for intermediate values of the mutual separation. In addition, initial investigations suggest that the frequency of oscillations of the system is greater by approximately 30% for larger separations than for smaller separations. We note that an increase of similar magnitude was also observed in experiment.

Simulating the dynamics and interactions of flexible fibers in Stokes flows

The dynamics of slender filaments or fibers suspended in Stokesian fluids are fundamental to understanding many flows arising in physics, biology and engineering. Such filaments can have aspect ratios of length to radius ranging from a few tens to several thousands. Full discretizations of such 3D flows are very costly. Instead, we employ a non-local slender body theory that yields an integral equation, along the filament centerline, relating the force exerted on the body to the filament velocity. This hydrodynamical description takes into account the effect of the filament on the fluid, and is extended to capture the interaction of multiple filaments as mediated by the intervening fluid. We consider filaments that are inextensible and elastic. Replacing the force in the slender body integral equation by an explicit expression that uses Euler–Bernoulli theory to model bending and tensile forces yields an integral expression for the velocity of the filament centerlines, coupled to auxiliary integro-differential equations for the filament tensions. Based on a regularized version of these slender body equations that is asymptotically equivalent to the original formulation, we construct a numerical method which uses a combination of finite differences, implicit time-stepping to avoid severe stability constraints, and special quadrature methods for nearly singular integrals. We present simulations of single flexible filaments, as well as multiple interacting filaments, evolving in a background shear flow. These simulations show shear induced buckling and relaxation of the filaments, leading to the storage and release of elastic energy. These dynamics are responsible for the development of positive first normal stress differences, commonly associated with visco-elastic fluids that are suspensions of microscopic elastic fibers.

Optical trap setup for measuring microtubule pushing forces

We present an optical trap design for force measurements of polymerizing microtubules. These stiff, filamentous cell components contribute to dynamic processes by generating pushing forces, for example during cell division. Although single traps are widely used for molecular pulling processes, studying pushing by flexible filaments requires extra measures. We introduce multiple, asymmetric traps for directional stabilization and bracing of the microtubules for enhanced rigidity. Our method performs in a force range which was inaccessible so far, namely near the stall force of a polymerizing microtubule. The described methods open the way to the study of other polymerizing biomolecular systems as well.

Dynamics of filaments: modelling the dynamics of driven microfilaments.

We describe a method for simulating the inertialess dynamics of a flexible filament immersed in a fluid. Typically, this regime is appropriate for filaments a few micrometres or less in size (flagella that propel micro-organisms for example). We apply the model to two systems; a filament that is wiggled at one end and planar swimming motion characteristic of simple spermatozoa. For the former we find qualitative agreement with theory. The shape is determined by a balance between bending and viscous forces and there is an optimal balance that maximizes the propulsion generated by this mechanism. Quantitatively we find less satisfactory agreement. For the spermatozoa, assuming a relatively naive bending mechanism in the form of a travelling force quadrupole wave, the model generates waveforms in very good agreement with experiment. This is only true, however, if the bending forces acting on the filament are large compared with the viscous forces. Experimental measurements of the tail stiffness imply this should not be the case. We discuss the implications of this observation in the context of the sperm's swimming mechanism.

Fabrication and compressive strength of macrochannelled tetragonal zirconia polycrystals with calcium phosphate coating layer

Macrochannelled tetragonal zirconia polycrystals (TZP) coated with a calcium phosphate layer were fabricated using a coextrusion process to produce strong and bioactive porous bioceramics. The initial feedrod, composed of three materials [TZP (shell), calcium phosphate (intermediate layer), and carbon black (core)], was coextruded through a 750-μm orifice at 120 °C, producing a continuous and flexible filament. Each sheet, which was composed of a unidirectional array of filaments, was stacked and then warm-pressed at 140 °C with 10 MPa. After binder burnout, the green billet was sintered between 1350 and 1600 °C for 1 h in air, leaving uniform macrochannels clad on the inside with bioactive calcium phosphate on a strong TZP body. The compressive strength of the specimen was much higher than that of calcium phosphate with a similar structure.

Interaction of two flapping filaments in a flowing soap film

Using the immersed boundary method, we have simulated the motion of two flexible filaments in a flowing soap film, which was experimentally studied by Zhang et al. [Nature (London) 408, 835 (2000)]. We found numerically two distinct modes of sustained oscillation of the two filaments: parallel flapping and mirror-image clapping, depending on the separation distance between the two filaments. Our simulation results agree with that of the experiment at least qualitatively, even though the Reynolds number of the flowing soap film in our simulation is about two orders of magnitude lower than that of the experiment.

Shock loading of fixed flexible thread and orthotropic elastic membrane

The main problems of the wave dynamics of flexible filaments and elastic membranes are solved. The reliability of the numerical algorithm proposed by the authors for calculating the elastic deformation of pneumatic structures under dynamic loading is confirmed when compared with the results of known studies obtained by analytical and numerical methods.

Computer simulations reveal motor properties generating stable antiparallel microtubule interactions.

An aster of microtubules is a set of flexible polar filaments with dynamic plus ends that irradiate from a common location at which the minus ends of the filaments are found. Processive soluble oligomeric motor complexes can bind simultaneously to two microtubules, and thus exert forces between two asters. Using computer simulations, I have explored systematically the possible steady-state regimes reached by two asters under the action of various kinds of oligomeric motors. As expected, motor complexes can induce the asters to fuse, for example when the complexes consist only of minus end–directed motors, or to fully separate, when the motors are plus end directed. More surprisingly, complexes made of two motors of opposite directionalities can also lead to antiparallel interactions between overlapping microtubules that are stable and sustained, like those seen in mitotic spindle structures. This suggests that such heterocomplexes could have a significant biological role, if they exist in the cell.

The role of disulfide bond in the amyloidogenic state of beta(2)-microglobulin studied by heteronuclear NMR.

beta(2)-Microglobulin (beta2-m) is a major component of dialysis-related amyloid fibrils. Although recombinant beta2-m forms needle-like fibrils by in vitro extension reaction at pH 2.5, reduced beta2-m, in which the intrachain disulfide bond is reduced, cannot form typical fibrils. Instead, thinner and flexible filaments are formed, as shown by atomic force microscopy images. To clarify the role of the disulfide bond in amyloid fibril formation, we characterized the conformations of the oxidized (intact) and reduced forms of beta2-m in the acid-denatured state at pH 2.5, as well as the native state at pH 6.5, by heteronuclear NMR. [(1)H]-(15)N NOE at the regions between the two cysteine residues (Cys25-Cys80) revealed a marked difference in the pico- and nanosecond time scale dynamics between that the acid-denatured oxidized and reduced states, with the former showing reduced mobility. Intriguingly, the secondary chemical shifts, DeltaCalpha, DeltaCO, and DeltaHalpha, and (3)J(HNHalpha) coupling constants indicated that both the oxidized and reduced beta2-m at pH 2.5 have marginal alpha-helical propensity at regions close to the C-terminal cysteine, although it is a beta-sheet protein in the native state. The results suggest that the reduced mobility of the denatured state is an important factor for the amylodogenic potential of beta2-m, and that the marginal helical propensity at the C-terminal regions might play a role in modifying this potential.