Hierarchically structured bioinspired nanocomposites.

Next-generation structural materials are expected to be lightweight, high-strength and tough composites with embedded functionalities to sense, adapt, self-repair, morph and restore. This Review highlights recent developments and concepts in bioinspired nanocomposites, emphasizing tailoring of the architecture, interphases and confinement to achieve dynamic and synergetic responses. We highlight cornerstone examples from natural materials with unique mechanical property combinations based on relatively simple building blocks produced in aqueous environments under ambient conditions. A particular focus is on structural hierarchies across multiple length scales to achieve multifunctionality and robustness. We further discuss recent advances, trends and emerging opportunities for combining biological and synthetic components, state-of-the-art characterization and modelling approaches to assess the physical principles underlying nature-inspired design and mechanical responses at multiple length scales. These multidisciplinary approaches promote the synergetic enhancement of individual materials properties and an improved predictive and prescriptive design of the next era of structural materials at multilength scales for a wide range of applications.

Characterizing the shear response of polymer-grafted nanoparticles.

Grafting polymer chains to the surface of nanoparticles overcomes the challenge of nanoparticle dispersion within nanocomposites and establishes high-volume fractions that are found to enable enhanced material mechanical properties. This study utilizes coarse-grained molecular dynamics simulations to quantify how the shear modulus of polymer-grafted nanoparticle (PGN) systems in their glassy state depends on parameters such as strain rate, nanoparticle size, grafting density, and chain length. The results are interpreted through further analysis of the dynamics of chain conformations and volume fraction arguments. The volume fraction of nanoparticles is found to be the most influential variable in deciding the shear modulus of PGN systems. A simple rule of mixture is utilized to express the monotonic dependence of shear modulus on the volume fraction of nanoparticles. Due to the reinforcing effect of nanoparticles, shortening the grafted chains results in a higher shear modulus in PGNs, which is not seen in linear systems. These results offer timely insight into calibrating molecular design parameters for achieving the desired mechanical properties in PGNs.

A new approach for extracting information from protein dynamics.

Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from network science. Most studies build protein dynamics networks from correlation measures, an approach that only works under very specific conditions, instead of the more robust inverse approach. Thus, we apply the inverse approach to the dynamics of protein dihedral angles, a system of internal coordinates, to avoid structural alignment. Using the well-characterized adhesion protein, FimH, we show that our method identifies networks that are physically interpretable, robust, and relevant to the allosteric pathway sites. We further use our approach to detect dynamical differences, despite structural similarity, for Siglec-8 in the immune system, and the SARS-CoV-2 spike protein. Our study demonstrates that using the inverse approach to extract a network from protein dynamics yields important biophysical insights.

The buckling-condensation mechanism driving gas vesicle collapse.

Gas vesicles (GVs) are proteinaceous cylindrical shells found within bacteria or archea growing in aqueous environments and are composed primarily of two proteins, gas vesicle protein A and C (GvpA and GvpC). GVs exhibit strong performance as next-generation ultrasound contrast agents due to their gas-filled interior, tunable collapse pressure, stability in vivo and functionalizable exterior. However, the exact mechanism leading to GV collapse remains inconclusive, which leads to difficulty in predicting collapse pressures for different species of GVs and in extending favorable nonlinear response regimes. Here, we propose a two stage mechanism leading to GV loss of echogenicity and rupture under hydrostatic pressure: elastic buckling of the cylindrical shell coupled with condensation driven weakening of the GV membrane. Our goal is to therefore test whether the final fracture of the GV membrane occurs by the interplay of both mechanisms or purely through buckling failure as previously believed. To do so, we (1) compare the theoretical condensation and buckling pressures with that for experimental GV collapse and (2) describe how condensation can lead to plastic buckling failure. GV shell properties that are necessary input to this theoretical description, such as the elastic moduli and wettability of GvpA, are determined using molecular dynamics simulations of a novel structural model of GvpA that better represents the hydrophobic core. For GVs that are not reinforced by GvpC, this analytical framework shows that the experimentally observed pressures resulting in loss of echogenicity coincide with both the elastic buckling and condensation pressure regimes. We also found that the stress strain curve for GvpA wetted on both the interior and exterior exhibits a loss of mechanical stability compared to GvpA only wetted on the exterior by the bulk solution. We identify a pressure vs. vesicle size regime where condensation can occur prior to buckling, which may preclude nonlinear shell buckling responses in contrast imaging.

Mesoscopic and multiscale modelling in materials.

The concept of multiscale modelling has emerged over the last few decades to describe procedures that seek to simulate continuum-scale behaviour using information gleaned from computational models of finer scales in the system, rather than resorting to empirical constitutive models. A large number of such methods have been developed, taking a range of approaches to bridging across multiple length and time scales. Here we introduce some of the key concepts of multiscale modelling and present a sampling of methods from across several categories of models, including techniques developed in recent years that integrate new fields such as machine learning and material design.

The effect of nanoparticle softness on the interfacial dynamics of a model polymer nanocomposite.

The introduction of soft organic nanoparticles (NPs) into polymer melts has recently expanded the material design space for polymer nanocomposites, compared to traditional nanocomposites that utilize rigid NPs, such as silica, metallic NPs, and other inorganic NPs. Despite advances in the fabrication and characterization of this new class of materials, the effect of NP stiffness on the polymer structure and dynamics has not been systematically investigated. Here, we use molecular dynamics to investigate the segmental dynamics of the polymer interfacial region of isolated NPs of variable stiffness in a polymer matrix. When the NP-polymer interactions are stronger than the polymer-polymer interactions, we find that the slowing of segmental dynamics in the interfacial region is more pronounced for stiff NPs. In contrast, when the NP-polymer interaction strength is smaller than the matrix interaction, the NP stiffness has relatively little impact on the changes in the polymer interfacial dynamics. We also find that the segmental relaxation time τα of segments in the NP interfacial region changes from values lower than to higher than the bulk material when the NP-polymer interaction strength is increased beyond a "critical" strength, reminiscent of a binding-unbinding transition. Both the NP stiffness and the polymer-surface interaction strength can thus greatly influence the relative segmental relaxation and interfacial mobility in comparison to the bulk material.

Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation.

Allostery governing two conformational states is one of the proposed mechanisms for catch-bond behavior in adhesive proteins. In FimH, a catch-bond protein expressed by pathogenic bacteria, separation of two domains disrupts inhibition by the pilin domain. Thus, tensile force can induce a conformational change in the lectin domain, from an inactive state to an active state with high affinity. To better understand allosteric inhibition in two-domain FimH (H2 inactive), we use molecular dynamics simulations to study the lectin domain alone, which has high affinity (HL active), and also the lectin domain stabilized in the low-affinity conformation by an Arg-60-Pro mutation (HL mutant). Because ligand-binding induces an allostery-like conformational change in HL mutant, this more experimentally tractable version has been proposed as a "minimal model" for FimH. We find that HL mutant has larger backbone fluctuations than both H2 inactive and HL active, at the binding pocket and allosteric interdomain region. We use an internal coordinate system of dihedral angles to identify protein regions with differences in backbone and side chain dynamics beyond the putative allosteric pathway sites. By characterizing HL mutant dynamics for the first time, we provide additional insight into the transmission of allosteric information across the lectin domain and build upon structural and thermodynamic data in the literature to further support the use of HL mutant as a "minimal model." Understanding how to alter protein dynamics to prevent the allosteric conformational change may guide drug development to prevent infection by blocking FimH adhesion.

Atomistic Modeling of Peptide Aggregation and ß-Sheet Structuring in Corn Zein for Viscoelasticity.

The structure-function relationships of plant-based proteins that give rise to desirable texture attributes in order to mimic meat products are generally unknown. In particular, it is not clear how to engineer viscoelasticity to impart cohesiveness and proper mouthfeel; however, it is known that intermolecular ß-sheet structures have the potential to enhance the viscoelastic property. Here, we investigated the propensity of selected peptide segments within common corn α-zein variants to maintain stable aggregates and ß-sheet structures. Simulations on dimer systems showed that stability was influenced by the initial orientation and the presence of contiguous small hydrophobic residues. Simulations using eight-peptide ß-sheet oligomers revealed that peptide sequences without proline had higher levels of ß-sheet structuring. Additionally, we identified that sequences with a dimer hydrogen-bonding density of >22% tended to have a larger percent ß-sheet conformation. These results contribute to understanding how the viscoelasticity of zein can be increased for use in plant-based meat analogues.

Organic Nanotube with Subnanometer, pH-Responsive Lumen.

While many synthetic nanotubes with a hydrophobic lumen and fast molecular transport have been developed, decorating the interior of these channels with polar and/or responsive functional groups remains challenging. In transmembrane proteins like the aquaporin and M2 channels, the presence of histidine residues in a mostly hydrophobic channel has led to enhanced selectivity and pH-based activation. Herein, we report the synthesis of Bzim-CP, a cyclic octapeptide that contains a benzimidazole functionality as a chemical and structural mimic of histidine. Bzim-CP undergoes different protonation states, forms subnanometer nanotubes, and projects two different ionizable functionalities into the lumen. Present studies open up synthetic possibilities to functionalize subnanometer porous channels as a basis toward understanding new transport phenomena.

Mechanical unfolding of alpha- and beta-helical protein motifs.

Alpha-helices and beta-sheets are the two most common secondary structure motifs in proteins. Beta-helical structures merge features of the two motifs, containing two or three beta-sheet faces connected by loops or turns in a single protein. Beta-helical structures form the basis of proteins with diverse mechanical functions such as bacterial adhesins, phage cell-puncture devices, antifreeze proteins, and extracellular matrices. Alpha-helices are commonly found in cellular and extracellular matrix components, whereas beta-helices such as curli fibrils are more common as bacterial and biofilm matrix components. It is currently not known whether it may be advantageous to use one helical motif over the other for different structural and mechanical functions. To better understand the mechanical implications of using different helix motifs in networks, here we use Steered Molecular Dynamics (SMD) simulations to mechanically unfold multiple alpha- and beta-helical proteins at constant velocity at the single molecule scale. We focus on the energy dissipated during unfolding as a means of comparison between proteins and work normalized by protein characteristics (initial and final length, # H-bonds, # residues, etc.). We find that although alpha-helices such as keratin and beta-helices CsgA and CsgB can require similar amounts of work to unfold, the normalized work per hydrogen bond, initial end to end length, and number of residues is greater for beta-helices at the same pulling rate. To explain this, we analyze the orientation of the backbone alpha carbons and backbone hydrogen bonds during unfolding. We find that the larger width and shorter height of beta-helices results in smaller angles between the protein backbone and the pulling direction during unfolding. As subsequent strands are separated from the beta-helix core, the angle between the backbone and the pulling direction diminishes. This marks a transition where beta-sheet hydrogen bonds become loaded predominantly in a collective shearing mode, which requires a larger rupture force. This finding underlines the importance of geometry in optimizing resistance to mechanical unfolding in proteins. The helix radius is identified here as an important parameter that governs how much sacrificial energy dissipation capacity can be stored in protein networks, where beta-helices offer unique properties.

Cohesive and adhesive properties of crosslinked semiflexible biopolymer networks.

Biomolecular semiflexible polymer networks with persistence lengths well above those of single polymeric chains serve important structural and adhesive roles in biology, biomaterials, food science and many other fields. While relationships between the structure and viscoelasticity of semiflexible polymer networks have been previously investigated, it remains challenging to systematically relate fibril and network properties to cohesive and adhesive properties that govern the function of these materials. To address this issue, here we utilize coarse-grained molecular dynamics simulations to thoroughly elucidate how the work of adhesion of a semiflexible polymer network to a surface depends on crosslink density and fibril persistence length. Two emergent characteristics of the network are its elasticity and its interfacial energy with the surface. Stiff networks that are either highly crosslinked or have high persistence length fibrils tend to have lower interfacial energy, and consequently, lower work of adhesion. For lightly crosslinked networks with flexible fibrils, considerable strain energy must be stored within the adhesive during detachment, which creates an additional penalty to detachment. Increasing persistence length while keeping crosslink density constant leads to porous, low density networks, leading to an optimal fibril persistence length at which maximum work of adhesion per mass density is attained for a given crosslink density. For any given fibril persistence length, increasing crosslink density has a slightly negative effect on network mass density and interfacial energy. A critical crosslink density is found, below which the networks have no significant load-bearing capacity. Lightly crosslinked networks above this threshold absorb more strain energy during desorption and consequently possess greater work of adhesion. The conflict between mass density and stiffness results in a non-monotonic trend between the ratio of work of adhesion to interfacial energy and persistence length. These findings provide physical insight into the adhesive mechanisms of biomaterials based on crosslinked semiflexible polymer networks, and reveal important design guidelines for bio-adhesives.

Temperature effects on the nanoindentation characterization of stiffness gradients in confined polymers.

The stiffening of polymers near inorganic fillers plays an important role in strengthening polymer nanocomposites, and recent advances in metrology have allowed us to sample such effects using local mechanical measurement techniques such as nanoindentation and atomic force microscopy. A general understanding of temperature and confinement effects on the measured stiffness gradient length-scale ξint is lacking however, which convolutes molecular interpretation of local property measurements. Using coarse-grained molecular dynamics and finite element nanoindentation simulations, we show that the measured ξint increases with temperature in highly confined polymer systems, a dependence which acts in the opposite direction in systems with low confinement. These disparate trends are closely related to the polymer's viscoelastic state and the resulting changes in incompressibility and dissipative ability as the polymer transitions from glassy to rubbery. At high temperatures above the glass transition temperature, a geometrically confined system restricts the viscous dissipation of the applied load by the increasingly incompressible polymer. The indentation causes a dramatic build-up of hydrostatic pressure near the confining surface, which contributes to an enlarged measurement of ξint. By contrast, a less-confined system allows the pressure to dissipate via intermolecular motion, thus lowering the measured ξint with increased temperature above the glass transition temperature. These findings suggest that the well-established thin film-nancomposite analogy for polymer mobility near interfaces can be convoluted when measuring local mechanical properties, as the viscoelastic state and geometric confinement of the polymer can affect the nanomechanical response during indentation purely from continuum effects.

Tunable seat belt behavior in nanocomposite interfaces inspired from bacterial adhesion pili.

A challenging problem in designing nanocomposites is to engineer nanoparticle interfaces that have tunable cohesive strength and rate-responsive behavior, for which inspiration can be taken from biological systems. An exemplary bio-interface is the Chaperone-Usher (CU) pili, such as type 1 expressed by bacteria Escherichia coli. The pili have unique biomechanical properties that enhance the ability of bacteria to sustain attachment to surfaces under large stresses, such as constant force extensibility, logarithmic velocity-uncoiling force dependence, and adhesive tips with catch bond behavior that exhibit longer bond life-times at greater force levels. Although biophysics of the pili under strain or stress is well-studied for anti-infective applications that aim to compromise pili adhesion, utilizing the biomechanical properties of the pili in material design applications is yet to be explored. In this work, we modeled the elongation of a single CU pilus with catch bond tip adhesin and examined its toughness response using Monte Carlo simulations. We showed that the pilus can act as a "molecular seat belt" that exhibits low toughness when pulled slowly and high toughness when pulled rapidly. Furthermore, we found that systematically varying the catch bond and shaft parameters leads to tunable seat belt behavior at the interface, where the sharpness of the transition from the low toughness to the high toughness regime and the velocity at the start of the transition can be dictated by molecular design parameters. Lastly, we tested the performance of CU pilus in slowing down a fast particle, and reveal that pili can effectively stop micron size projectiles with high initial velocities. The molecular seat belt mechanism presented here provides insight into how nanocomposite interfaces can be engineered to create molecular networks with linkers that switch on or off depending on strain rate.

Biomimetic engineering of conductive curli protein films.

Bioelectronic systems derived from peptides and proteins are of particular interest for fabricating novel flexible, biocompatible and bioactive devices. These synthetic or recombinant systems designed for mediating electron transport often mimic the proteinaceous appendages of naturally occurring electroactive bacteria. Drawing inspiration from such conductive proteins with a high content of aromatic residues, we have engineered a fibrous protein scaffold, curli fibers produced by Escherichia coli bacteria, to enable long-range electron transport. We report the genetic engineering and characterization of curli fibers containing aromatic residues of different nature, with defined spatial positioning, and with varying content on single self-assembling CsgA curli subunits. Our results demonstrate the impressive versatility of the CsgA protein for genetically engineering protein-based materials with new functions. Through a scalable purification process, we show that macroscopic gels and films can be produced, with engineered thin films exhibiting a greater conductivity compared with wild-type curli films. We anticipate that this engineered conductive scaffold, and our approach that combines computational modeling, protein engineering, and biosynthetic manufacture will contribute to the improvement of a range of useful bio-hybrid technologies.

Sub-20 nm Stable Micelles Based on a Mixture of Coiled-Coils: A Platform for Controlled Ligand Presentation.

Ligand-functionalized, multivalent nanoparticles have been extensively studied for biomedical applications from imaging agents to drug delivery vehicles. However, the ligand cluster size is usually heterogeneous and the local valency is ill-defined. Here, we present a mixed micelle platform hierarchically self-assembled from a mixture of two amphiphilic 3-helix and 4-helix peptide-polyethylene glycol (PEG)-lipid hybrid conjugates. We demonstrate that the local multivalent ligand cluster size on the micelle surface can be controlled based on the coiled-coil oligomeric state. The oligomeric states of mixed peptide bundles were found to be in their individual native states. Similarly, mixed micelles indicate the orthogonal self-association of coiled-coil amphiphiles. Using differential scanning calorimetry, fluorescence recovery spectroscopy, and coarse-grained molecular dynamics simulation, we studied the distribution of coiled-coil bundles within the mixed micelles and observed migration of coiled-coils into nanodomains within the sub-20 nm mixed micelle. This report provides important insights into the assembly and formation of nanophase-separated micelles with precise control over the local multivalent state of ligands on the micelle surface.

Bending energy penalty enhances the adhesive strength of functional amyloid curli to surfaces.

The functional amyloid curli fiber, a major proteinaceous component of biofilm extracellular matrices, plays an important role in biofilm formation and enterobacteriaceae adhesion. Curli nanofibers exhibit exceptional underwater adhesion to various surfaces, have high rigidity and strong tensile mechanical properties, and thus hold great promise in biomaterials. The mechanisms of how curli fibers strongly attach to surfaces and detach under force remain elusive. To investigate curli fiber adhesion to surfaces, we developed a coarse-grained curli fiber model, in which the protein subunit CsgA (curli specific gene A) self-assembles into the fiber. The coarse-grained model yields physiologically relevant and tunable bending rigidity and persistence length. The force-induced desorption of a single curli fiber is examined using coarse-grained modeling and theoretical analysis. We find that the bending energy penalty arising from high persistence length enhances the resistance of the curli fiber against desorption and thus strengthens the adhesion of the curli fiber to surfaces. The CsgA-surface adhesion energy and the curli fiber bending rigidity both play crucial roles in the resistance of curli fiber against desorption from surfaces. To enable the desorption process, the applied peeling force must overcome both the interfacial adhesion energy and the energy barrier for bending the curli fiber at the peeling front. We show that the energy barrier to desorption increases with the interfacial adhesion energy, however, the bending induced failure of a single curli fiber limits the work of adhesion if the proportion of the CsgA-surface adhesion energy to the CsgA-CsgA cohesive energy becomes large. These results illustrate that the optimal adhesion performance of nanofibers is dictated by the interplay between bending, surface energy and cohesive energy. Our model provides timely insight into enterobacteriaceae adhesion mechanisms as well as future designs of engineered curli fiber based adhesives.

Plasticity resulted from phase transformation for monolayer molybdenum disulfide film during nanoindentation simulations.

Molecular dynamics simulations on nanoindentation of circular monolayer molybdenum disulfide (MoS2) film are carried out to elucidate the deformation and failure mechanisms. Typical force-deflection curves are obtained, and in-plane stiffness of MoS2 is extracted according to a continuum mechanics model. The measured in-plane stiffness of monolayer MoS2 is about 182 ± 14 N m-1, corresponding to an effective Young's modulus of 280 ± 21 GPa. More interestingly, at a critical indentation depth, the loading force decreases sharply and then increases again. The loading-unloading-reloading processes at different initial unloading deflections are also conducted to explain the phenomenon. It is found that prior to the critical depth, the monolayer MoS2 film can return to the original state after completely unloading, while there is hysteresis when unloading after the critical depth and residual deformation exists after indenter fully retracted, indicating plasticity. This residual deformation is found to be caused by the changed lattice structure of the MoS2, i.e. a phase transformation. The critical pressure to induce the phase transformation is then calculated to be 36 ± 2 GPa, consistent with other studies. Finally, the influences of temperature, the diameter and indentation rate of MoS2 monolayer on the mechanical properties are also investigated.

Side-group size effects on interfaces and glass formation in supported polymer thin films.

Recent studies on glass-forming polymers near interfaces have emphasized the importance of molecular features such as chain stiffness, side-groups, molecular packing, and associated changes in fragility as key factors that govern the magnitude of Tg changes with respect to the bulk in polymer thin films. However, how such molecular features are coupled with substrate and free surface effects on Tg in thin films remains to be fully understood. Here, we employ a chemically specific coarse-grained polymer model for methacrylates to investigate the role of side-group volume on glass formation in bulk polymers and supported thin films. Our results show that bulkier side-groups lead to higher bulk Tg and fragility and are associated with a pronounced free surface effect on overall Tg depression. By probing local Tg within the films, however, we find that the polymers with bulkier side-groups experience a reduced confinement-induced increase in local Tg near a strongly interacting substrate. Further analyses indicate that this is due to the packing frustration of chains near the substrate interface, which lowers the attractive interactions with the substrate and thus lessens the surface-induced reduction in segmental mobility. Our results reveal that the size of the polymer side-group may be a design element that controls the confinement effects induced by the free surface and substrates in supported polymer thin films. Our analyses provide new insights into the factors governing polymer dynamics in bulk and confined environments.

Internal Structure of 15 nm 3-Helix Micelle Revealed by Small-Angle Neutron Scattering and Coarse-Grained MD Simulation.

3-Helix micelles (3HM) formed by self-assembly of peptide-polymer conjugate amphiphiles have shown promise as a nanocarrier platform due to their long-circulation, deep tumor penetration, selective accumulation in tumor, and ability to cross the blood-brain barrier (BBB) for glioblastoma therapy. There is a need to understand the structural contribution to the high in vivo stability and performance of 3HM. Using selective deuteration, the contrast variation technique in small-angle neutron scattering, and coarse-grained molecular dynamics simulation, we determined the spatial distribution of each component within 3HM. Our results show a slightly deformed polyethylene glycol (PEG) conformation within the micelle that is radially offset from its conjugation site toward the exterior of the micelle and a highly solvated shell. Surprisingly, ∼85 v/v % of 3HM is water, unusually higher than any micellar nanocarrier based on our knowledge. The result will provide important structural insights for future studies to uncover the molecular origin of 3HM's in vivo performance, and development of the nanocarriers.