Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.

Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest that it is connected to the phenomenon of 'clogging' in soft matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.

Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence.

Many viruses employ ATP-powered motors during assembly to translocate DNA into procapsid shells. Previous reports raise the question if motor function is modulated by substrate DNA sequence: (i) the phage T4 motor exhibits large translocation rate fluctuations and pauses and slips; (ii) evidence suggests that the phage phi29 motor contacts DNA bases during translocation; and (iii) one theoretical model, the 'B-A scrunchworm', predicts that 'A-philic' sequences that transition more easily to A-form would alter motor function. Here, we use single-molecule optical tweezers measurements to compare translocation of phage, plasmid, and synthetic A-philic, GC rich sequences by the T4 motor. We observed no significant differences in motor velocities, even with A-philic sequences predicted to show higher translocation rate at high applied force. We also observed no significant changes in motor pausing and only modest changes in slipping. To more generally test for sequence dependence, we conducted correlation analyses across pairs of packaging events. No significant correlations in packaging rate, pausing or slipping versus sequence position were detected across repeated measurements with several different DNA sequences. These studies suggest that viral genome packaging is insensitive to DNA sequence and fluctuations in packaging motor velocity, pausing and slipping are primarily stochastic temporal events.

Evidence that a catalytic glutamate and an 'Arginine Toggle' act in concert to mediate ATP hydrolysis and mechanochemical coupling in a viral DNA packaging motor.

ASCE ATPases include ring-translocases such as cellular helicases and viral DNA packaging motors (terminases). These motors have conserved Walker A and B motifs that bind Mg2+-ATP and a catalytic carboxylate that activates water for hydrolysis. Here we demonstrate that Glu179 serves as the catalytic carboxylate in bacteriophage λ terminase and probe its mechanistic role. All changes of Glu179 are lethal: non-conservative changes abrogate ATP hydrolysis and DNA translocation, while the conservative E179D change attenuates ATP hydrolysis and alters single molecule translocation dynamics, consistent with a slowed chemical hydrolysis step. Molecular dynamics simulations of several homologous terminases suggest a novel mechanism, supported by experiments, wherein the conserved Walker A arginine 'toggles' between interacting with a glutamate residue in the 'lid' subdomain and the catalytic glutamate upon ATP binding; this switch helps mediate a transition from an 'open' state to a 'closed' state that tightly binds nucleotide and DNA, and also positions the catalytic glutamate next to the γ-phosphate to align the hydrolysis transition state. Concomitant reorientation of the lid subdomain may mediate mechanochemical coupling of ATP hydrolysis and DNA translocation. Given the strong conservation of these structural elements in terminase enzymes, this mechanism may be universal for viral packaging motors.

Identification of a rapidly formed nonnucleosomal histone-DNA intermediate that is converted into chromatin by ACF.

Chromatin assembly involves the combined action of histone chaperones and ATP-dependent motor proteins. Here, we investigate the mechanism of nucleosome assembly with a purified chromatin assembly system containing the histone chaperone NAP1 and the ATP-dependent motor protein ACF. These studies revealed the rapid formation of a stable nonnucleosomal histone-DNA intermediate that is converted into canonical nucleosomes by ACF. The histone-DNA intermediate does not supercoil DNA like a canonical nucleosome, but has a nucleosome-like appearance by atomic force microscopy. This intermediate contains all four core histones, lacks NAP1, and is formed by the initial deposition of histones H3-H4. Conversion of the intermediate into histone H1-containing chromatin results in increased resistance to micrococcal nuclease digestion. These findings suggest that the histone-DNA intermediate corresponds to nascent nucleosome-like structures, such as those observed at DNA replication forks. Related complexes might be formed during other chromatin-directed processes such as transcription, DNA repair, and histone exchange.

Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging.

Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.

Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA.

We report evidence for an unconventional type of allosteric regulation of a biomotor. We show that the genome-packaging motor of phage ϕ29 is regulated by a sensor that detects the density and conformation of the DNA packaged inside the viral capsid, and slows the motor by a mechanism distinct from the effect of a direct load force on the motor. Specifically, we show that motor-ATP interactions are regulated by a signal that is propagated allosterically from inside the viral shell to the motor mounted on the outside. This signal continuously regulates the motor speed and pausing in response to changes in either density or conformation of the packaged DNA, and slows the motor before the buildup of large forces resisting DNA confinement. Analysis of motor slipping reveals that the force resisting packaging remains low (<1 pN) until ∼ 70% and then rises sharply to ∼ 23 pN at high filling, which is a several-fold lower value than was previously estimated under the assumption that force alone slows the motor. These findings are consistent with recent studies of the stepping kinetics of the motor. The allosteric regulatory mechanism we report allows double-stranded DNA viruses to achieve rapid, high-density packing of their genomes by limiting the buildup of nonequilibrium load forces on the motor.

Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29.

We use optical tweezers to study the effect of attractive versus repulsive DNA-DNA interactions on motor-driven viral packaging. Screening of repulsive interactions accelerates packaging, but induction of attractive interactions by spermidine(3+) causes heterogeneous dynamics. Acceleration is observed in a fraction of complexes, but most exhibit slowing and stalling, suggesting that attractive interactions promote nonequilibrium DNA conformations that impede the motor. Thus, repulsive interactions facilitate packaging despite increasing the energy of the theoretical optimum spooled DNA conformation.

Systematic Evaluation of Adhesion and Fracture Toughness in Multi-Material Fused Deposition Material Extrusion.

Material extrusion (MEX) additive manufacturing has successfully fabricated assembly-free structures composed of different materials processed in the same manufacturing cycle. Materials with different mechanical properties can be employed for the fabrication of bio-inspired structures (i.e., stiff materials connected to soft materials), which are appealing for many fields, such as bio-medical and soft robotics. In the present paper, process parameters and 3D printing strategies are presented to improve the interfacial adhesion between carbon fiber-reinforced nylon (CFPA) and thermoplastic polyurethane (TPU), which are extruded in the same manufacturing cycle using a multi-material MEX setup. To achieve our goal, a double cantilever beam (DCB) test was used to evaluate the mode I fracture toughness. The results show that the application of a heating gun (assembled near the nozzle) provides a statistically significant increase in mean fracture toughness energy from 12.3 kJ/m2 to 33.4 kJ/m2. The underlying mechanism driving this finding was further investigated by quantifying porosity at the multi-material interface using an X-ray computed tomography (CT) system, in addition to quantifying thermal history. The results show that using both bead ironing and the hot air gun during the printing process leads to a reduction of 24% in the average void volume fraction. The findings from the DCB test and X-ray CT analysis agree well with the polymer healing theory, in which an increased thermal history led to an increased fracture toughness at the multi-material interface. Moreover, this study considers the thermal history of each printed layer to correlate the measured debonding energy with results obtained using the reptation theory.

Cerebrospinal fluid flow extends to peripheral nerves further unifying the nervous system.

Cerebrospinal fluid (CSF) is responsible for maintaining brain homeostasis through nutrient delivery and waste removal for the central nervous system (CNS). Here, we demonstrate extensive CSF flow throughout the peripheral nervous system (PNS) by tracing distribution of multimodal 1.9-nanometer gold nanoparticles, roughly the size of CSF circulating proteins, infused within the lateral cerebral ventricle (a primary site of CSF production). CSF-infused 1.9-nanometer gold transitions from CNS to PNS at root attachment/transition zones and distributes through the perineurium and endoneurium, with ultimate delivery to axoplasm of distal peripheral nerves. Larger 15-nanometer gold fails to transit from CNS to PNS and instead forms "dye-cuffs," as predicted by current dogma of CSF restriction within CNS, identifying size limitations in central to peripheral flow. Intravenous 1.9-nanometer gold is unable to cross the blood-brain/nerve barrier. Our findings suggest that CSF plays a consistent role in maintaining homeostasis throughout the nervous system with implications for CNS and PNS therapy and neural drug delivery.

Role of DNA-DNA sliding friction and non-equilibrium dynamics in viral genome ejection and packaging.

Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics, and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest it is connected to the phenomenon of "clogging" in soft-matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.

Cerebrospinal Fluid Flow Extends to Peripheral Nerves.

Cerebrospinal fluid (CSF) is an aqueous solution responsible for nutrient delivery and waste removal for the central nervous system (CNS). The three-layer meningeal coverings of the CNS support CSF flow. Peripheral nerves have an analogous three-layer covering consisting of the epineurium, perineurium, and endoneurium. Peripheral axons, located in the inner endoneurium, are bathed in "endoneurial fluid" similar to CSF but of undefined origin. CSF flow in the peripheral nervous system has not been demonstrated. Here we show CSF flow extends beyond the CNS to peripheral nerves in a contiguous flowing system. Utilizing gold nanoparticles, we identified that CSF is continuous with the endoneurial fluid and reveal the endoneurial space as the likely site of CSF flow in the periphery. Nanogold distribution along entire peripheral nerves and within their axoplasm suggests CSF plays a role in nutrient delivery and waste clearance, fundamental aspects of peripheral nerve health and disease. One Sentence Summary: Cerebrospinal fluid unites the nervous system by extending beyond the central nervous system into peripheral nerves.

Single-molecule studies of viral DNA packaging.

Many double-stranded DNA bacteriophages and viruses use specialized ATP-driven molecular machines to package their genomes into tightly confined procapsid shells. Over the last decade, single-molecule approaches - and in particular, optical tweezers - have made key contributions to our understanding of this remarkable process. In this chapter, we review these advances and the insights they have provided on the packaging mechanisms of three bacteriophages: φ 29, λ, and T4.

The Q motif of a viral packaging motor governs its force generation and communicates ATP recognition to DNA interaction.

A key step in the assembly of many viruses is the packaging of DNA into preformed procapsids by an ATP-powered molecular motor. To shed light on the motor mechanism we used single-molecule optical tweezers measurements to study the effect of mutations in the large terminase subunit in bacteriophage lambda on packaging motor dynamics. A mutation, K84A, in the putative ATPase domain driving DNA translocation was found to decrease motor velocity by approximately 40% but did not change the force dependence or decrease processivity substantially. These findings support the hypothesis that a deviant "Walker A-like" phosphate-binding motif lies adjacent to residue 84. Another mutation, Y46F, was also found to decrease motor velocity by approximately 40% but also increase slipping during DNA translocation by >10-fold. These findings support the hypothesis that viral DNA packaging motors contain an adenine-binding motif that regulates ATP hydrolysis and substrate affinity analogous to the "Q motif" recently identified in DEAD-box RNA helicases. We also find impaired force generation for the Y46F mutant, which shows that the Q motif plays an important role in determining the power and efficiency of the packaging motor.

Effect of Process Parameters on Void Distribution, Volume Fraction, and Sphericity within the Bead Microstructure of Large-Area Additive Manufacturing Polymer Composites.

Short carbon fiber-reinforced composite materials produced by large-area additive manufacturing (LAAM) are attractive due to their lightweight, favorable mechanical properties, multifunctional applications, and low manufacturing costs. However, the physical and mechanical properties of short carbon-fiber-reinforced composites 3D printed via LAAM systems remain below expectations due in part to the void formation within the bead microstructure. This study aimed to assess void characteristics including volume fraction and sphericity within the microstructure of 13 wt% short carbon fiber acrylonitrile butadiene styrene (SCF/ABS). Our study evaluated SCF/ABS as a pellet, a single freely extruded strand, a regularly deposited single bead, and a single bead manufactured with a roller during the printing process using a high-resolution 3D micro-computed tomography (µCT) system. Micro voids were shown to exist within the microstructure of the SCF/ABS pellet and tended to become more prevalent in a single freely extruded strand which showed the highest void volume fraction among all the samples studied. Results also showed that deposition on the print bed reduced the void volume fraction and applying a roller during the printing process caused a further reduction in the void volume fraction. This study also reports the void's shape within the microstructure in terms of sphericity which indicated that SCF/ABS single freely extruded strands had the highest mean void sphericity (voids tend to be more spherical). Moreover, this study evaluated the effect of printing process parameters, including nozzle temperature, extrusion speed and nozzle height above the printing table on the void volume fraction and sphericity within the microstructure of regularly deposited single beads.

A Review on Microstructural Formations of Discontinuous Fiber-Reinforced Polymer Composites Prepared via Material Extrusion Additive Manufacturing: Fiber Orientation, Fiber Attrition, and Micro-Voids Distribution.

A discontinuous fiber-reinforced polymer composite (DFRPC) provides superior mechanical performances in material extrusion additive manufacturing (MEAM) parts, and thus promotes their implementations in engineering applications. However, the process-induced structural defects of DFRPCs increase the probability of pre-mature failures as the manufactured parts experience complicated external loads. In light of this, the meso-structures of the MEAM parts have been discussed previously, while systematic analyses reviewing the studies of the micro-structural formations of the composites are limited. This paper summarizes the current state-of-the-art in exploring the correlations between the MEAM processes and the associated micro-structures of the produced composites. Experimental studies and numerical analyses including fiber orientation, fiber attrition, and micro-voids are collected and discussed. Based on the review and parametric study results, it is considered that the theories and numerical characterizations on fiber length attrition and micro-porosities within the MEAM-produced composites are in high demand, which is a potential topic for further explorations.

Mutations altering a structurally conserved loop-helix-loop region of a viral packaging motor change DNA translocation velocity and processivity.

Many double-stranded DNA viruses employ ATP-driven motors to translocate their genomes into small, preformed viral capsids against large forces resisting confinement. Here, we show via direct single-molecule measurements that a mutation T194M downstream of the Walker B motif in the phage lambda gpA packaging motor causes an 8-fold reduction in translocation velocity without substantially changing processivity or force dependence, whereas the mutation G212S in the putative C (coupling) motif causes a 3-fold reduction in velocity and a 6-fold reduction in processivity. Meanwhile a T194M pseudorevertant (T194V) showed a near restoration of the wild-type dynamics. Structural comparisons and modeling show that these mutations are in a loop-helix-loop region that positions the key residues of the catalytic motifs, Walker B and C, in the ATPase center and is structurally homologous with analogous regions in chromosome transporters and SF2 RNA helicases. Together with recently published studies of SpoIIIE chromosome transporter and Ded1 RNA helicase mutants, these findings suggest the presence of a structurally conserved region that may be a part of the mechanism that determines motor velocity and processivity in several different types of nucleic acid translocases.

A Fully Coupled Simulation of Planar Deposition Flow and Fiber Orientation in Polymer Composites Additive Manufacturing.

Numerical studies for polymer composites deposition additive manufacturing have provided significant insight promoting the rapid development of the technology. However, little of existing literature addresses the complex yet important polymer composite melt flow-fiber orientation coupling during deposition. This paper explores the effect of flow-fiber interaction for polymer deposition of 13 wt.% Carbon Fiber filled Acrylonitrile Butadiene Styrene (CF/ABS) composites through a finite-element-based numerical approach. The molten composite flow in the extrusion die plus a strand of the deposited bead contacting the deposition substrate is modelled using a 2D isothermal and incompressible Newtonian planar flow model, where the material deposition rate is ~110 mm/s simulating a large scale additive manufacturing process. The Folgar-Tucker model associated with the Advani-Tucker orientation tensor approach is adopted for the evaluation of the fiber orientation state, where the orthotropic fitted closure is applied. By comparing the computed results between the uncoupled and fully coupled solutions, it is found that the flow-orientation effects are mostly seen in the nozzle convergence zone and the extrusion-deposition transition zone of the flow domain. Further, the fully coupled fiber orientation solution is highly sensitive to the choice of the fiber-fiber interaction coefficient CI, e.g., assigning CI as 0.01 and 0.001 results in a 23% partial relative difference in the predicted elastic modulus along deposition direction. In addition, Structural properties of deposited CF/ABS beads based on our predicted fiber orientation results show favorable agreements with related experimental studies.

Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers.

We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25-45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.

Evaluation of the chondral modeling theory using fe-simulation and numeric shape optimization.

The chondral modeling theory proposes that hydrostatic pressure within articular cartilage regulates joint size, shape, and congruence through regional variations in rates of tissue proliferation. The purpose of this study is to develop a computational model using a nonlinear two-dimensional finite element analysis in conjunction with numeric shape optimization to evaluate the chondral modeling theory. The model employed in this analysis is generated from an MR image of the medial portion of the tibiofemoral joint in a subadult male. Stress-regulated morphological changes are simulated until skeletal maturity and evaluated against the chondral modeling theory. The computed results are found to support the chondral modeling theory. The shape-optimized model exhibits increased joint congruence, broader stress distributions in articular cartilage, and a relative decrease in joint diameter. The results for the computational model correspond well with experimental data and provide valuable insights into the mechanical determinants of joint growth. The model also provides a crucial first step toward developing a comprehensive model that can be employed to test the influence of mechanical variables on joint conformation.

Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >107-fold decrease in phage yield, but we identified nine mutants with partial activity. Several were cold-sensitive, suggesting that mobility of the residues is important. Single-molecule measurements showed that the partially active A175L exhibits a small reduction in motor velocity and increase in slipping, consistent with a slowed ATP binding transition, whereas G176S exhibits decreased slipping, consistent with an accelerated transition. All changes to the conserved D178, predicted to coordinate Mg2+•ATP, were lethal except conservative change D178E. Biochemical interrogation of the inactive D178N protein found no folding or assembly defects and near-normal endonuclease activity, but a ∼200-fold reduction in steady-state ATPase activity, a lag in the single-turnover ATPase time course, and no DNA packaging, consistent with a critical role in ATP-coupled DNA translocation. Molecular dynamics simulations of related enzymes suggest that the aspartate plays an important role in enhancing the catalytic activity of the motor by bridging the Walker motifs and precisely contributing its charged group to help polarize the bound nucleotide. Supporting this prediction, single-molecule measurements revealed that change D178E reduces motor velocity without increasing slipping, consistent with a slowed hydrolysis step. Our studies thus illuminate the mechanistic roles of Walker-B residues in ATP binding, hydrolysis, and DNA translocation by this powerful motor.