The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes.

Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.

The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation.

Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.

Encapsulating therapeutic cells in RGD-modified agarose microcapsules.

Current cell-based strategies for repairing damaged tissue often show limited efficacy due to low cell retention at the site of injury. Encapsulation of cells within hydrogel microcapsules demonstrably increases cell retention but benefits can be limited due to premature cell escape from the hydrogel microcapsules and subsequent clearance from the targeted tissue. We propose a method of encapsulating cells in agarose microcapsules that have been modified to increase cell retention by providing cell attachment domains within the agarose hydrogel allowing cells to adhere to the microcapsules. We covalently modified agarose with the addition of the cell adhesion peptide, RGD (arginine, glycine, aspartic acid). We then used a microfluidic platform to encapsulate single cells within 50 µm agarose microcapsules. We tracked encapsulated cells for cell viability, egress from microcapsules and attachment to microcapsules at 2 h, 24 h, and 48 h after encapsulation. Many encapsulated cells eventually egress their microcapsule. Those that were encapsulated using RGD-modified agarose adhered to the outer surface of the microcapsule following egress. NIH 3T3 cells showed nearly 45% of egressed cells attached to the outside of RGD modified agarose microcapsules, while minimal cellular adhesion was observed when using unmodified agarose. Similarly, human umbilical vein endothelial cells had up to 33% of egressed cells attached and explant-derived cardiac cells showed up to 20% attachment with the presence of RGD binding domains within the agarose microcapsules.

Investigation of the yielding transition in concentrated colloidal systems via rheo-XPCS.

We probe the microstructural yielding dynamics of a concentrated colloidal system by performing creep/recovery tests with simultaneous collection of coherent scattering data via X-ray Photon Correlation Spectroscopy (XPCS). This combination of rheology and scattering allows for time-resolved observations of the microstructural dynamics as yielding occurs, which can be linked back to the applied rheological deformation to form structure-property relations. Under sufficiently small applied creep stresses, examination of the correlation in the flow direction reveals that the scattering response recorrelates with its predeformed state, indicating nearly complete microstructural recovery, and the dynamics of the system under these conditions slows considerably. Conversely, larger creep stresses increase the speed of the dynamics under both applied creep and recovery. The data show a strong connection between the microstructural dynamics and the acquisition of unrecoverable strain. By comparing this relationship to that predicted from homogeneous, affine shearing, we find that the yielding transition in concentrated colloidal systems is highly heterogeneous on the microstructural level.

Enhanced Collagen-like Protein for Facile Biomaterial Fabrication.

We present a collagen-mimetic protein of bacterial origin based upon a modified subdomain of the collagen-like Sc12 protein from Streptococcus pyogenes, as an alternative collagen-like biomaterial platform that is highly soluble, forms stable, homogeneous, fluid-like solutions at elevated concentrations, and that can be efficiently fabricated into hydrogel materials over a broad range of pH conditions. This extended bacterial collagen-like (eBCL) protein is expressed in a bacterial host and purified as a trimeric assembly exhibiting a triple helical secondary structure in its collagen-like subdomain that is stable near physiological solution conditions (neutral pH and 37 °C), as well as over a broad range of pH conditions. We also show how this sequence can be modified to include biofunctional attributes, in particular, the Arg-Gly-Asp (RGD) sequence to elicit integrin-specific cell binding, without loss of structural function. Furthermore, through the use of EDC-NHS chemistry, we demonstrate that members of this eBCL protein system can be covalently cross-linked to fabricate transparent hydrogels with high protein concentrations (at least to 20% w/w). These hydrogels are shown to possess material properties and resistance to enzymatic degradation that are comparable or superior to a type I collagen control. Moreover, such hydrogels containing the constructs with the RGD integrin-binding sequence are shown to promote the adhesion, spreading, and proliferation of C2C12 and 3T3 cells in vitro. Due to its enhanced solubility, structural stability, fluidity at elevated concentrations, ease of modification, and facility of cross-linking, this eBCL collagen-mimetic system has potential for numerous biomedical material applications, where the ease of processing and fabrication and the facility to tailor the sequence for specific biological functionality are desired.

Microscopic ergodicity breaking governs the emergence and evolution of elasticity in glass-forming nanoclay suspensions.

We report a study combining x-ray photon correlation spectroscopy (XPCS) with in situ rheology to investigate the microscopic dynamics and mechanical properties of aqueous suspensions of the synthetic hectorite clay Laponite, which is composed of charged, nanometer-scale, disk-shaped particles. The suspensions, with particle concentrations ranging from 3.25 to 3.75 wt %, evolve over time from a fluid to a soft glass that displays aging behavior. The XPCS measurements characterize the localization of the particles during the formation and aging of the soft-glass state. The fraction of localized particles, f_{0}, increases rapidly during the early formation stage and grows more slowly during subsequent aging, while the characteristic localization length r_{loc} steadily decreases. Despite the strongly varying rates of aging at different concentrations, both f_{0} and r_{loc} scale with the elastic shear modulus G^{'} in a manner independent of concentration. During the later aging stage, the scaling between r_{loc} and G^{'} agrees quantitatively with a prediction of naive mode coupling theory. Breakdown of agreement with the theory during the early formation stage indicates the prevalence of dynamic heterogeneity, suggesting the soft solid forms through precursors of dynamically localized clusters.

Time dependent stress relaxation and recovery in mechanically strained 3D microtissues.

Characterizing the time-dependent mechanical properties of cells is not only necessary to determine how they deform but also to understand how external forces trigger biochemical-signaling cascades to govern their behavior. At present, mechanical properties are largely assessed by applying local shear or compressive forces on single cells grown in isolation on non-physiological 2D surfaces. In comparison, we developed the microfabricated vacuum actuated stretcher to measure tensile loading of 3D multicellular "microtissue" cultures. Using this approach, we here assessed the time-dependent stress relaxation and recovery responses of microtissues and quantified the spatial viscoelastic deformation following step length changes. Unlike previous results, stress relaxation and recovery in microtissues measured over a range of step amplitudes and pharmacological treatments followed an augmented stretched exponential behavior describing a broad distribution of inter-related timescales. Furthermore, despite the variety of experimental conditions, all responses led to a single linear relationship between the residual elastic stress and the degree of stress relaxation, suggesting that these mechanical properties are coupled through interactions between structural elements and the association of cells with their matrix. Finally, although stress relaxation could be quantitatively and spatially linked to recovery, they differed greatly in their dynamics; while stress recovery acted as a linear process, relaxation time constants changed with an inverse power law with the step size. This assessment of microtissues offers insights into how the collective behavior of cells in a 3D collagen matrix generates the dynamic mechanical properties of tissues, which is necessary to understand how cells deform and sense mechanical forces in vivo.

Relationship between rheology and structure of interpenetrating, deforming and compressing microgels.

Thermosensitive microgels are widely studied hybrid systems combining properties of polymers and colloidal particles in a unique way. Due to their complex morphology, their interactions and packing, and consequentially the viscoelasticity of suspensions made from microgels, are still not fully understood, in particular under dense packing conditions. Here we study the frequency-dependent linear viscoelastic properties of dense suspensions of micron sized soft particles in conjunction with an analysis of the local particle structure and morphology based on superresolution microscopy. By identifying the dominating mechanisms that control the elastic and dissipative response, we can explain the rheology of these widely studied soft particle assemblies from the onset of elasticity deep into the overpacked regime. Interestingly, our results suggest that the friction between the microgels is reduced due to lubrification mediated by the polymer brush-like corona before the onset of interpenetration.

Interaction-free ghost-imaging of structured objects.

Quantum - or classically correlated - light can be employed in various ways to improve resolution and measurement sensitivity. In an "interaction-free" measurement, a single photon can be used to reveal the presence of an object placed within one arm of an interferometer without being absorbed by it. With a technique known as "ghost-imaging", entangled photon pairs are used for detecting an opaque object with significantly improved signal-to-noise ratio while preventing over-illumination. Here, we integrate these two methods to obtain a new imaging technique which we term "interaction-free ghost-imaging" (IFGI). With this new technique, we reduce photon illumination on the object by up to 26.5% while still maintaining at least the same image quality of conventional ghost-imaging. Alternatively, IFGI can improve image signal-to-noise ratio by 18% when given the same number of interacting photons as in standard ghost-imaging. IFGI is also sensitive to phase and polarisation changes of the photons introduced by a structured object. These advantages make IFGI superior for probing light-sensitive materials and biological tissues.

Enhanced gel formation in binary mixtures of nanocolloids with short-range attraction.

Colloidal suspensions transform between fluid and disordered solid states as parameters such as the colloid volume fraction and the strength and nature of the colloidal interactions are varied. Seemingly subtle changes in the characteristics of the colloids can markedly alter the mechanical rigidity and flow behavior of these soft composite materials. This sensitivity creates both a scientific challenge and an opportunity for designing suspensions for specific applications. In this paper, we report a novel mechanism of gel formation in mixtures of weakly attractive nanocolloids with modest size ratio. Employing a combination of x-ray photon correlation spectroscopy, rheometry, and molecular dynamics simulations, we find that gels are stable at remarkably weaker attraction in mixtures with size ratio near two than in the corresponding monodisperse suspensions. In contrast with depletion-driven gelation at larger size ratio, gel formation in the mixtures is triggered by microphase demixing of the species into dense regions of immobile smaller colloids surrounded by clusters of mobile larger colloids that is not predicted by mean-field thermodynamic considerations. These results point to a new route for tailoring nanostructured colloidal solids through judicious combination of interparticle interaction and size distribution.

Measuring mechanodynamics in an unsupported epithelial monolayer grown at an air-water interface.

Actomyosin contraction and relaxation in a monolayer is a fundamental biophysical process in development and homeostasis. Current methods used to characterize the mechanodynamics of monolayers often involve cells grown on solid supports such as glass or gels. The results of these studies are fundamentally influenced by these supporting structures. Here we describe a new method for measuring the mechanodynamics of epithelial monolayers by culturing cells at an air-liquid interface. These model monolayers are grown in the absence of any supporting structures, removing cell-substrate effects. This method's potential was evaluated by observing and quantifying the generation and release of internal stresses upon actomyosin contraction (800 ± 100 Pa) and relaxation (600 ± 100 Pa) in response to chemical treatments. Although unsupported monolayers exhibited clear major and minor strain axes, they were not correlated with nuclear alignment as observed when the monolayers were grown on soft deformable gels. It was also observed that both gels and glass substrates led to the promotion of long-range cell nuclei alignment not seen in the hanging-drop model. This new approach provides us with a picture of basal actomyosin mechanodynamics in a simplified system, allowing us to infer how the presence of a substrate affects contractility and long-range multicellular organization and dynamics.

Electrochemically Directed Assembly of Designer Coiled-Coil Telechelic Proteins.

We report the design and characterization of a de novo electrogelation protein comprising a central spider silk glue motif flanked by terminal pH-triggered coiled-coil domains. The coiled-coiled domains were designed to form intramolecular helix bundles below a sharply defined pH-trigger point (∼pH 5.3), whereas the spider silk glue protein, because of its substantial Glu content, serves both as an anionic electrophoretic transport element at neutral and elevated pH and as a disordered linker chain between the associated helix bundles at reduced pH. We show that in an electrochemical cell, a solution of these telechelic proteins migrates toward the anode where the terminal coiled-coil domains are triggered to form coiled-coil assemblies that act as transient cross-links for the e-gel state. Upon cessation of the current, the coiled-coil domains become denatured and the e-gel transforms back into a fluid solution of polypeptides in a fully reversible manner. This simplified triblock protein design mimics many of the characteristics of more complex electrogelation proteins, such as silk fibroin. As such, it provides some insight into possible general mechanisms of protein electrogelation. Moreover, this general class of electrogelation proteins has the potential for biomedical applications of electrochemically triggered gelation, such as externally switchable delivery of therapeutic cell and drugs from a responsive matrix.

Tyrosine Templating in the Self-Assembly and Crystallization of Silk Fibroin.

Native silk fibers exhibit strength and toughness that rival those of the best synthetic fibers. Despite significant research, further insight is still needed to understand the mechanisms by which silkworms are capable of spinning such tough fibers. Here we propose that π-π and π-OH group interactions of tyrosine side chains provide templating effects, such that the crystal-forming domains are in registration, thereby fostering the self-assembly of the spinning dope. Intrinsic fluorescence measurements, in conjunction with circular dichroism, showed that during self-assembly of regenerated silk solutions, the tyrosine residues were localized in a more hydrophobic local environment, suggesting preferential assembly. In situ Fourier transform infrared spectroscopy indicated that cross-linking of the tyrosine residues resulted in the development of extended ß-sheet structure. Additionally, control of cross-link density directly influenced the degree of crystallinity upon drying. Molecular dynamics simulations were performed on silk mimetic peptides in order to more thoroughly understand the role of tyrosines. The results indicated that tyrosine residues tended to transiently colocate in solution due to π-π interactions and hydrogen bonds with adjacent residues and with the peptide backbone. These more stable tyrosine interactions resulted in reduced lateral chain fluctuations and increased incidence of coordinated intrachain association, while introduction of a dityrosine bond directly promoted the formation of ß-sheet structures. In total, the experimental and modeling data support a critical role for tyrosine-tyrosine interactions as a key early feature in the self-assembly of regenerated silk protein chains and therefore are important in the robust and unusual mechanical properties ultimately achieved in the process.

Extracellular Forces Cause the Nucleus to Deform in a Highly Controlled Anisotropic Manner.

Physical forces arising in the extra-cellular environment have a profound impact on cell fate and gene regulation; however the underlying biophysical mechanisms that control this sensitivity remain elusive. It is hypothesized that gene expression may be influenced by the physical deformation of the nucleus in response to force. Here, using 3T3s as a model, we demonstrate that extra-cellular forces cause cell nuclei to rapidly deform (<1 s) preferentially along their shorter nuclear axis, in an anisotropic manner. Nuclear anisotropy is shown to be regulated by the cytoskeleton within intact cells, with actin and microtubules resistant to orthonormal strains. Importantly, nuclear anisotropy is intrinsic, and observed in isolated nuclei. The sensitivity of this behaviour is influenced by chromatin organization and lamin-A expression. An anisotropic response to force was also highly conserved amongst an array of examined nuclei from differentiated and undifferentiated cell types. Although the functional purpose of this conserved material property remains elusive, it may provide a mechanism through which mechanical cues in the microenvironment are rapidly transmitted to the genome.

Simulating the entropic collapse of coarse-grained chromosomes.

Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.

Echoes in x-ray speckles track nanometer-scale plastic events in colloidal gels under shear.

We report x-ray photon correlation spectroscopy experiments on a concentrated nanocolloidal gel subject to in situ oscillatory shear strain. The strain causes periodic echoes in the speckle pattern that lead to peaks in the intensity autocorrelation function. Above a threshold strain that is near the first yield point of the gel, the peak amplitude decays exponentially with the number of shear cycles, signaling irreversible particle rearrangements. The wave-vector dependence of the decay rate reveals a power-law distribution in the size of regions undergoing shear-induced rearrangement. The gel also displays strain softening well below the threshold, indicating a range of strains at which the rheology is nonlinear but the microscopic deformations are reversible.

Coarse-grained molecular dynamics simulations of depletion-induced interactions for soft matter systems.

Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics (MD) simulation approaches appropriate for the study of complex systems. This paper examines the use of two common truncated Lennard-Jones (Weeks-Chandler-Andersen (WCA)) potentials to describe a pair of colloidal particles in a thermal bath of depletants. The shifted-WCA model is the steeper of the two repulsive potentials considered, while the combinatorial-WCA model is the softer. It is found that the depletion-induced well depth for the combinatorial-WCA model is significantly deeper than the shifted-WCA model because the resulting overlap of the colloids yields extra accessible volume for depletants. For both shifted- and combinatorial-WCA simulations, the second virial coefficients and pair potentials between colloids are demonstrated to be well approximated by the Morphometric Thermodynamics (MT) model. This agreement suggests that the presence of depletants can be accurately modelled in MD simulations by implicitly including them through simple, analytical MT forms for depletion-induced interactions. Although both WCA potentials are found to be effective generic coarse-grained simulation approaches for studying depletion effects in complicated soft matter systems, combinatorial-WCA is the more efficient approach as depletion effects are enhanced at lower depletant densities. The findings indicate that for soft matter systems that are better modelled by potentials with some compressibility, predictions from hard-sphere systems could greatly underestimate the magnitude of depletion effects at a given depletant density.

Spatial-spectral coupling in coherent anti-Stokes Raman scattering microscopy.

Coherent anti-Stokes Raman scattering (CARS) microscopy is a third-order nonlinear optical technique which permits label-free, molecule-specific hyperspectral imaging. The interference between coherent resonant and non-resonant terms leads to well known distortions in the vibrational spectrum, requiring the use of retrieval algorithms. It also leads to spatial imaging distortions, largely due to the Gouy phase, when objects are smaller than the Rayleigh range. Here we consider that the focal position and spectral contributions to the nonlinear image formation are intrinsically coupled and cannot be corrected by conventional retrieval methods.

Simulations of free-solution electrophoresis of polyelectrolytes with a finite Debye length using the Debye-Hückel approximation.

We introduce a mesoscale simulation method based on multiparticle collision dynamics (MPCD) for the electrohydrodynamics of polyelectrolytes with finite Debye lengths. By applying the Debye-Hückel approximation to assign an effective charge to MPCD particles near charged monomers, our simulations are able to reproduce the rapid rise in the electrophoretic mobility with respect to the degree of polymerization for the shortest polymer lengths followed by a small decrease for longer polymers due to charge condensation. Moreover, these simulations demonstrate the importance of a finite Debye length in accurately determining the mobility of uniformly charged polyelectrolytes and net neutral polyampholytes.