Nature designs tough collagen: explaining the nanostructure of collagen fibrils

Unraveling the molecular mechanism of collagen flexibility during physiological warmup using molecular dynamics simulation and machine learning

Physiological warmup plays an important role in reducing the injury risk in different sports. In response to the associated temperature increase, the muscle and tendon soften and become easily stretched. In this study, we focused on type I collagen, the main component of the Achilles tendon, to unveil the molecular mechanism of collagen flexibility upon slight heating and to develop a model to predict the strain of collagen sequences. We used molecular dynamics approaches to simulate the molecular structures and mechanical behavior of the gap and overlap regions in type I collagen at 307 K, 310 K, and 313 K. The results showed that the molecular model in the overlap region is more sensitive to temperature increases. Upon increasing the temperature by 3 degrees Celsius, the end-to-end distance and Young's modulus of the overlap region decreased by 5% and 29.4%, respectively. The overlap region became more flexible than the gap region at higher temperatures. GAP-GPA and GNK-GSK triplets are critical for providing molecular flexibility upon heating. A machine learning model developed from the molecular dynamics simulation results showed good performance in predicting the strain of collagen sequences at a physiological warmup temperature. The strain-predictive model could be applied to future collagen designs to obtain desirable temperature-dependent mechanical properties.

Lamellar thickness measurements in control and osteogenesis imperfecta human bone, with development of a method of automated thickness averaging to simplify quantitation

Lamellar bone that forms in moderate and severe osteogenesis imperfecta (OI) is composed of structurally irregular lamellae compared to those in control bone. OI and control cortical bone fragments were prepared for light microscopy in standardized fashion: decalcified, embedded in plastic, sectioned and stained with toluidine blue. Polarization light microscopy (PLM) was used to demonstrate and quantify bright and dark lamellar thicknesses in cortical bone fragments from 5 patients with moderate to severe OI in whom type I collagen structural/molecular defects were detected and in control bone from 5 patients. Rigid selection criteria identified lamellar regions for quantification. Thicknesses of bright and dark lamellae were measured manually at 20X magnification using a histomorphometric image analysis system. A method of automated thickness averaging was developed to determine lamellar thicknesses from PLM images to make measurement faster. Our study demonstrates, for the first time, that in OI bone from patients with type I collagen structural/molecular defects mean lamellar thickness measurements (along with the bright and dark lamellar thicknesses) were less than those in control bone by statistically highly significant differences. The mean value for bright lamellae was less than that for dark lamellae in both control and OI bone. The ratio of mean values for bright/dark lamellar thicknesses was the same in control and OI bone. The automated method obtained similar results to the manual method. Lamellar bone in moderate and severe OI with type I collagen defects is composed of thinner and less structurally regular lamellae than those in control bone. This finding indicates that lamellar thickness measurements can be helpful in assessing the effect of specific collagen and collagen-related mutations on OI bone synthesis and warrant inclusion in research and clinical histomorphometric assessments.

Preparation of collagen fibrils from mineralized tissues and evaluation by atomic force microscopy

Mineralized tissues like bone and dentin are materials that support the distribution of mechanical loads through the body of humans and other animals. While their organic content plays a critical role on the structural behavior of these materials, investigations that quantify the structural properties of collagen fibrils in mineralized tissues at the nanoscale are rather limited. We report a new experimental methodology to prepare samples of dentinal collagen fibrils for evaluation by atomic force microscopy and characterize their mechanical behavior. Specifically, a Dynamic Mechanical Analysis (DMA) of the collagen fibrils was performed to study their viscoelastic behavior. The capacity for viscous dampening in the fibrils was characterized in terms of measures of the energy dissipation, phase angle and loss modulus in both the peak and trough regions of the fibrils. According to the phase angle and the loss modulus, the peak regions of the fibrils exhibit significantly greater stiffness and capacity for dampening than the trough regions. This new approach will help in exploring the role of collagen fibrils in the mechanical behavior of dentin and other mineralized tissues as well as help to understand the potential effects from changes in fibril confirmation with tissue treatments, aging or that result from chronic disease.

Surrogate modeling of articular cartilage degradation to understand the synergistic role of MMP-1 and MMP-9: a case study

A characteristic feature of arthritic diseases is cartilage extracellular matrix (ECM) degradation, often orchestrated by the overexpression of matrix metalloproteinases (MMPs) and other proteases. The interplay between fibril level degradation and the tissue-level aggregate response to biomechanical loading was explored in this work by a computational multiscale cartilaginous model. We considered the relative abundance of collagenases (MMP-1) and gelatinases (MMP-9) in surrogate models, where the diffusion (spatial distribution) of these enzymes and the subsequent, co-localized fibrillar damage were spatially randomized with Latin Hypercube Sampling. The computational model was constructed by incorporating the results from prior molecular dynamics simulations (tensile test) of microfibril degradation into a hyper-elastoplastic fibril-reinforced cartilage model. Including MMPs-mediated collagen fibril-level degradation in computational models may help understand the ECM pathomechanics at the tissue level. The mechanics of cartilage tissue and fibril show variations in mechanical integrity depending on the different combinations of MMPs-1 and 9 with a concentration ratio of 1:1, 3:1, and 1:3 in simulated indentation tests. The fibril yield (local failure) was initiated at 20.2 ± 3.0 (%) and at 23.0 ± 2.8 (%) of bulk strain for col 1:gel 3 and col 3: gel 1, respectively. The reduction in failure stress (global response) was 39.8% for col 1:gel 3, 37.5% for col 1:gel 1, and 36.7% for col 3:gel 1 compared with the failure stress of the degradation free tissue. These findings indicate that cartilage's global and local mechanisms of failure largely depend on the relative abundance of the two key enzymes-collagenase (MMP-1) and gelatinase (MMP-9) and the spatial characteristics of diffusion across the layers of the cartilage ECM.

The influence of AGEs and enzymatic cross-links on the mechanical properties of collagen fibrils

Cross-links are considered to be a key component of collagen fibrils as they can change the fibrillar behavior in various ways. Advanced-Glycation Endproducts (AGEs), one particular type of cross-links, have been shown to accumulate and impair the mechanical properties of collageneous tissues, whereas enzymatic cross-links (ECLs) are known for stabilizing the structure of the fibril. However, the reasons for whether a given type of cross-link improves or impairs the material properties remain unknown. Here, we use coarse-grained steered molecular models to evaluate the effect of AGEs and ECLs cross-links content on the deformation and failure properties of collagen fibrils. Our simulations show that the collagen fibrils stiffen at high strain levels when the AGEs content exceeds a critical value. In addition, the strength of the fibril increases with AGEs accumulation. By analyzing the forces within the different types of cross-links (AGEs and ECLs) as well as their failure, we demonstrate that a change of deformation mechanism is at the origin of these observations. A high AGEs content reinforces force transfer through AGEs cross-links rather than through friction between sliding tropocollagen molecules. We show that this failure mechanism, which is associated with lower energy dissipation, results in more abrupt failure of the collagen fibril. Our results provide a direct and causal link between increased AGEs content, inhibited intra-fibrillar sliding, increased stiffness, and abrupt fibril fracture. Therefore, they explain the mechanical origin of bone brittleness as commonly observed in elderly and diabetic populations. Our findings contribute to a better understanding of the mechanisms underlying impaired tissue behaviour due to elevated AGEs content and could enable targeted measures regarding the reduction of specific collagen cross-linking levels.

Two-Dimensional Peptide Assembly via Arene-Perfluoroarene Interactions for Proliferation and Differentiation of Myoblasts

Supramolecular assembly based on aromatic interactions can provide well-defined nanostructures with an understanding of intermolecular interactions at the molecular level. The peptide assembly via a supramolecular approach can overcome the inherent limitations of bioactive peptides, such as proteolytic degradations and rapid internalizations into the cytosol. Although extensive research has been carried out on supramolecular peptide materials with a two-dimensional (2D) structure, more needs to be reported on biological activity studies using well-defined 2D peptide materials. Physical and chemical properties of the 2D peptide assembly attributed to their large surface area and flexibility can show low cytotoxicity, enhanced molecular loading, and higher bioconjugation efficiency in biological applications. Here, we report supramolecular 2D materials based on the pyrene-grafted amphiphilic peptide, which contains a peptide sequence (Asp-Gly-Glu-Ala; DGEA) that is reported to bind to the integrin α2β1 receptor in 2D cell membranes. The addition of octafluoronaphthalene (OFN) to the pyrene-grafted peptide could induce a well-ordered 2D assembly by face-centered arene-perfluoroarene stacking. The DGEA-peptide 2D assembly with a flat structure, structural stability against enzymatic degradations, and a larger size can enhance the proliferation and differentiation of muscle cells via continuous interactions with cell membrane receptors integrin α2β1 showing a low intracellular uptake (15%) compared to that (62%) of the vesicular peptide assembly. These supramolecular approaches via the arene-perfluoroarene interaction provide a strategy to fabricate well-defined 2D peptide materials with an understanding of assembly at the molecular level for the next-generation peptide materials.

Collagen Derived from Fish Industry Waste: Progresses and Challenges

Fish collagen garnered significant academic and commercial focus in the last decades featuring prospective applications in a variety of health-related industries, including food, medicine, pharmaceutics, and cosmetics. Due to its distinct advantages over mammalian-based collagen, including the reduced zoonosis transmission risk, the absence of cultural-religious limitations, the cost-effectiveness of manufacturing process, and its superior bioavailability, the use of collagen derived from fish wastes (i.e., skin, scales) quickly expanded. Moreover, by-products are low cost and the need to minimize fish industry waste's environmental impact paved the way for the use of discards in the development of collagen-based products with remarkable added value. This review summarizes the recent advances in the valorization of fish industry wastes for the extraction of collagen used in several applications. Issues related to processing and characterization of collagen were presented. Moreover, an overview of the most relevant applications in food industry, nutraceutical, cosmetics, tissue engineering, and food packaging of the last three years was introduced. Lastly, the fish-collagen market and the open technological challenges to a reliable recovery and exploitation of this biopolymer were discussed.

Chemical bonds in collagen rupture selectively under tensile stress

Collagen fibres are the main constituent of the extracellular matrix, and fulfil an important role in the structural stability of living multicellular organisms. An open question is how collagen absorbs pulling forces, and if the applied forces are strong enough to break bonds, what mechanisms underlie this process. As experimental studies on this topic are challenging, simulations are an important tool to further our understanding of these mechanisms. Here, we present pulling simulations of collagen triple helices, revealing the molecular mechanisms induced by tensile stress. At lower forces, pulling alters the configuration of proline residues leading to an effective absorption of applied stress. When forces are strong enough to introduce bond ruptures, these are located preferentially in X-position residues. Reduced backbone flexibility, for example through mutations or cross linking, weakens tensile resistance, leading to localised ruptures around these perturbations. In fibre-like segments, a significant overrepresentation of ruptures in proline residues compared to amino acid contents is observed. This study confirms the important role of proline in the structural stability of collagen, and adds detailed insight into the molecular mechanisms underlying this observation.

Optically Active Nanomaterials and Its Biosensing Applications-A Review

This article discusses optically active nanomaterials and their optical biosensing applications. In addition to enhancing their sensitivity, these nanomaterials also increase their biocompatibility. For this reason, nanomaterials, particularly those based on their chemical compositions, such as carbon-based nanomaterials, inorganic-based nanomaterials, organic-based nanomaterials, and composite-based nanomaterials for biosensing applications are investigated thoroughly. These nanomaterials are used extensively in the field of fiber optic biosensing to improve response time, detection limit, and nature of specificity. Consequently, this article describes contemporary and application-based research that will be of great use to researchers in the nanomaterial-based optical sensing field. The difficulties encountered during the synthesis, characterization, and application of nanomaterials are also enumerated, and their future prospects are outlined for the reader's benefit.

Modulation of the biophysical and biochemical properties of collagen by glycation for tissue engineering applications

The structural and functional properties of collagen are modulated by the presence of intramolecular and intermolecular crosslinks. Advanced Glycation End-products (AGEs) can produce intermolecular crosslinks by bonding the free amino groups of neighbouring proteins. In this research, the following hypothesis is explored: The accumulation of AGEs in collagen decreases its proteolytic degradation rates while increasing its stiffness. Fluorescence Lifetime Imaging (FLIM) and Fourier-transform infrared spectroscopy (FTIR) detect biochemical changes in collagen scaffolds during the glycation process. The accumulation of AGEs increases exponentially in the collagen scaffolds as a function of Methylglyoxal (MGO) concentration by performing autofluorescence measurement and competitive ELISA. Glycated scaffolds absorb water at a much higher rate confirming the direct affinity between AGEs and interstitial water within collagen fibrils. In addition, the topology of collagen fibrils as observed by Atomic Force Microscopy (AFM) is a lot more defined following glycation. The elastic modulus of collagen fibrils decreases as a function of glycation, whereas the elastic modulus of collagen scaffolds increases. Finally, the enzymatic degradation of collagen by bacterial collagenase shows a sigmoidal pattern with a much slower degradation rate in the glycated scaffolds. This study identifies unique variations in the properties of collagen following the accumulation of AGEs. STATEMENT OF SIGNIFICANCE: In humans, Advanced Glycation End-products (AGEs) are naturally produced as a result of aging process. There is an evident lack of knowledge in the basic science literature explaining the biomechanical impact of AGE-mediated crosslinks on the functional and structural properties of collagen at both the nanoscale (single fibrils) and mesoscale (bundles of fibrils). This research, demonstrates how it is possible to harness this natural phenomenon in vitro to enhance the properties of engineered collagen fibrils and scaffolds. This study identifies unique variations in the properties of collagen at nanoscale and mesoscale following accumulation of AGEs. In their approach, they investigate the unique properties conferred to collagen, namely enhanced water sorption, differential elastic modulus, and finally sigmoidal proteolytic degradation behavior.

Bioinspired Impact-Resistant and Self-Monitoring Nanofibrous Composites

Lightweight and impact-resistant materials with self-monitoring capability are highly desired for protective applications, but are challenging to be artificially fabricated. Herein, a scalable-manufactured aramid nanofiber (ANF)-based composite combining these key properties is presented. Inspired by the strengthening and toughening mechanisms relying on recoverable interfaces commonly existing in biological composites, mechanically weak but dense hydrogen bonds are introduced into the ANF interfaces to achieve simultaneously enhanced tensile strength (300 MPa), toughness (55 MJ m^-3 ), and impact resistance of the nanofibrous composite. The achieved mechanical property combination displays attractive advantages compared with that of most of previously reported nanocomposites. Additionally, the nanofibrous composite is designed with a capability for real-time self-monitoring of its structural safety during both quasi-static tensile and dynamic impact processes, based on the strain/damage-induced resistance variations of a conductive nanowire network inside it. These comprehensive properties enable the present nanofibrous composite with promising potential for protective applications.

Electrospun-Reinforced Suturable Biodegradable Artificial Cornea

Despite rigorous investigations, the hydrogels currently available to replace damaged tissues, such as the cornea, cannot fulfill mechanical and structural requirements and, more importantly, cannot be sutured into host tissues due to the lack of hierarchical structures to dissipate exerted stress. In this report, solution electrospinning of polycaprolactone (PCL), protein-based hydrogel perfusion, and layer-by-layer stacking are used to generate a hydrogel-microfiber composite with varying PCL fiber diameters and hydrogel concentrations. Integrating PCL microfibers into the hydrogel synergistically improves the mechanical properties and suturability of the construct up to 10-fold and 50-fold, respectively, compared to the hydrogel and microfiber scaffolds alone, approaching those of the corneal tissue. Human corneal cells cultured on composites are viable and can spread, proliferate, and retain phenotypic characteristics. Moreover, corneal stromal cells migrate into the scaffold, degrade it, and regenerate the extracellular matrix. The current hydrogel reinforcing system paves the way for producing suturable and, therefore, transplantable tissue constructs with desired mechanical properties.

Mechanics of isolated individual collagen fibrils

Collagen fibrils are the fundamental structural elements in vertebrate animals and compose a framework that provides mechanical support to load-bearing tissues. Understanding how these fibrils initially form and mechanically function has been the focus of a myriad of detailed investigations over the last few decades. From these studies a great amount of knowledge has been acquired as well as a number of new questions to consider. In this review, we examine the current state of our knowledge of the mechanical properties of extant fibrils. We emphasize on the mechanical response and related deformation of collagen fibrils upon tension, which is the predominant load imposed in most collagen-rich tissues. We also illuminate the gaps in knowledge originating from the intriguing results that the field is still trying to interpret. STATEMENT OF SIGNIFICANCE: : Collagen is the result of millions of years of biological evolution and is a unique family of proteins, the majority of which provide mechanical support to biological tissues. Cells produce collagen molecules that self-assemble into larger structures, known as collagen fibrils. As simple as they appear under an optical microscope, collagen fibrils display a complex ultrastructural architecture tuned to the external forces that are imposed upon them. Even more complex is the way collagen fibrils deform under loading, and the nature of the mechanisms that drive their formation in the first place. Here, we present a cogent synthesis of the state-of-knowledge of collagen fibril mechanics. We focus on the information we have from in vitro experiments on individual, isolated from tissues, collagen fibrils and the knowledge available from in silico tests.

Multiscale modeling of skin mechanical Behavior: Effect of dehydrating agent on Collagen's mechanical properties

The dermis, second layer of human skin, is mainly responsible for mechanical response of the skin. The unique viscoelastic nature of this layer arises from the characteristic hierarchical structure of collagen at various length scales. The effect of topical formulation on skin's mechanical properties of great importance for several personal-care applications. Understanding the transport of an active ingredient across skin layer and its effects on the structure of collagen assembly is crucial for successful design of these applications. In this study, we report a multiscale modelling framework mimicking the skin's mechanical behavior. The framework captures the details from the nanoscale (tropocollagen) to microscale (fibers). At first, atomistic molecular dynamics simulations (MDS) of tropocollagen (TC) molecules of various lengths (∼100 nm) were performed to obtain the molecular modulus of TC. The stress-strain response data obtained from these simulations, were utilized in macroscopic models of fibrils and fibers. The modulus obtained from the mentioned framework was in good agreement with earlier reported experimental data. Further, we have utilized this framework to show the effect of dehydrating agent on skin's mechanical response. The hydration effect is utilized in many anti-ageing strategies to improve the overall mechanical property of skin. We showed that on incorporation of hydrating agent, the collagen structure changes significantly at molecular scale which effects the overall response of the skin at macroscopic scale. The reported multiscale framework can further be explored to gain insights into interlinked properties of collagen at much larger scales without extensive molecular simulations and detailed experiments.

Hierarchical Structure and Properties of the Bone at Nano Level

Bone is a highly hierarchical complex structure that consists of organic and mineral components represented by collagen molecules (CM) and hydroxyapatite crystals (HAC), respectively. The nanostructure of bone can significantly affect its mechanical properties. There is a lack of understanding how collagen fibrils (CF) in different orientations may affect the mechanical properties of the bone. The objective of this study is to investigate the effect of interaction, orientation, and hydration on atomic models of the bone composed of collagen helix (CH) and HAC, using molecular dynamics simulations and therefrom bone-related disease origins. The results demonstrate that the mechanical properties of the bone are affected significantly by the orientation of the CF attributed to contact areas at 0° and 90° models. The molecular dynamics simulation illustrated that there is significant difference (p < 0.005) in the ultimate tensile strength and toughness with respect to the orientation of the hydrated and un-hydrated CF. Additionally, the results indicated that having the force in a longitudinal direction (0°) provides more strength compared with the CF in the perpendicular direction (90°). Furthermore, the results show that substituting glycine (GLY) with any other amino acid affects the mechanical properties and strength of the CH, collagen−hydroxyapatite interface, and eventually affects the HAC. Generally, hydration dramatically influences bone tissue elastic properties, and any change in the orientation or any abnormality in the atomic structure of either the CM or the HAC would be the main reason of the fragility in the bone, affecting bone pathology.

Design of synthetic collagens that assemble into supramolecular banded fibers as a functional biomaterial testbed

Collagens are the most abundant proteins of the extracellular matrix, and the hierarchical folding and supramolecular assembly of collagens into banded fibers is essential for mediating cell-matrix interactions and tissue mechanics. Collagen extracted from animal tissues is a valuable commodity, but suffers from safety and purity issues, limiting its biomaterials applications. Synthetic collagen biomaterials could address these issues, but their construction requires molecular-level control of folding and supramolecular assembly into ordered banded fibers, comparable to those of natural collagens. Here, we show an innovative class of banded fiber-forming synthetic collagens that recapitulate the morphology and some biological properties of natural collagens. The synthetic collagens comprise a functional-driver module that is flanked by adhesive modules that effectively promote their supramolecular assembly. Multiscale simulations support a plausible molecular-level mechanism of supramolecular assembly, allowing precise design of banded fiber morphology. We also experimentally demonstrate that synthetic fibers stimulate osteoblast differentiation at levels comparable to natural collagen. This work thus deepens understanding of collagen biology and disease by providing a ready source of safe, functional biomaterials that bridge the current gap between the simplicity of peptide biophysical models and the complexity of in vivo animal systems.

Human endothelial cells form an endothelium in freestanding collagen hollow filaments fabricated by direct extrusion printing

Fiber-shaped materials have great potential for tissue engineering applications as they provide structural support and spatial patterns within a three-dimensional construct. Here we demonstrate the fabrication of mechanically stable, meter-long collagen hollow filaments by a direct extrusion printing process. The fibres are permeable for oxygen and proteins and allow cultivation of primary human endothelial cells (ECs) at the inner surface under perfused conditions. The cells show typical characteristics of a well-organized EC lining including VE-cadherin expression, cellular response to flow and ECM production. The results demonstrate that the collagen tubes are capable of creating robust soft tissue filaments. The mechanical properties and the biofunctionality of these collagen hollow filaments facilitate the engineering of prevascularised tissue engineering constructs.

Polycrystalline Diamond Coating on Orthopedic Implants: Realization and Role of Surface Topology and Chemistry in Adsorption of Proteins and Cell Proliferation

Polycrystalline diamond has the potential to improve the osseointegration of orthopedic implants compared to conventional materials such as titanium. However, despite the excellent biocompatibility and superior mechanical properties, the major challenge of using diamond for implants, such as those used for hip arthroplasty, is the limitation of microwave plasma chemical vapor deposition (CVD) techniques to synthesize diamond on complex-shaped objects. Here, for the first time, we demonstrate diamond growth on titanium acetabular shells using the surface wave plasma CVD method. Polycrystalline diamond coatings were synthesized at low temperatures (∼400 °C) on three types of acetabular shells with different surface structures and porosities. We achieved the growth of diamond on highly porous surfaces designed to mimic the structure of the trabecular bone and improve osseointegration. Biocompatibility was investigated on nanocrystalline diamond (NCD) and ultrananocrystalline diamond (UNCD) coatings terminated either with hydrogen or oxygen. To understand the role of diamond surface topology and chemistry in the attachment and proliferation of mammalian cells, we investigated the adsorption of extracellular matrix proteins and monitored the metabolic activity of fibroblasts, osteoblasts, and bone-marrow-derived mesenchymal stem cells (MSCs). The interaction of bovine serum albumin and type I collagen with the diamond surfaces was investigated by confocal fluorescence lifetime imaging microscopy (FLIM). We found that the proliferation of osteogenic cells was better on hydrogen-terminated UNCD than on the oxygen-terminated counterpart. These findings correlated with the behavior of collagen on diamond substrates observed by FLIM. Hydrogen-terminated UNCD provided better adhesion and proliferation of osteogenic cells, compared to titanium, while the growth of fibroblasts was poorest on hydrogen-terminated NCD and MSCs behaved similarly on all tested surfaces. These results open new opportunities for application of diamond coatings on orthopedic implants to further improve bone fixation and osseointegration.

Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation

Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing collagen effectively during materials processing ex vivo and subsequent function in vivo requires stability over wide temperature ranges to avoid denaturation and loss of structure, measured as melting temperature (T_m). Although significant research has been conducted on understanding how collagen primary amino acid sequences correspond to T_m values, a robust framework to facilitate the design of collagen sequences with specific T_m remains a challenge. Here, we develop a general model using a genetic algorithm within a deep learning framework to design collagen sequences with specific T_m values. We report 1,000 de novo collagen sequences, and we show that we can efficiently use this model to generate collagen sequences and verify their T_m values using both experimental and computational methods. We find that the model accurately predicts T_m values within a few degrees centigrade. Further, using this model, we conduct a high-throughput study to identify the most frequently occurring collagen triplets that can be directly incorporated into collagen. We further discovered that the number of hydrogen bonds within collagen calculated with molecular dynamics (MD) is directly correlated to the experimental measurement of triple-helical quality. Ultimately, we see this work as a critical step to helping researchers develop collagen sequences with specific T_m values for intended materials manufacturing methods and biomedical applications, realizing a mechanistic materials by design paradigm.

Extracellular matrix mechanobiology in cancer cell migration

The extracellular matrix (ECM) is pivotal in modulating tumor progression. Besides chemically stimulating tumor cells, it also offers physical support that orchestrates the sequence of events in the metastatic cascade upon dynamically modulating cell mechanosensation. Understanding this translation between matrix biophysical cues and intracellular signaling has led to rapid growth in the interdisciplinary field of cancer mechanobiology in the last decade. Substantial efforts have been made to develop novel in vitro tumor mimicking platforms to visualize and quantify the mechanical forces within the tissue that dictate tumor cell invasion and metastatic growth. This review highlights recent findings on tumor matrix biophysical cues such as fibrillar arrangement, crosslinking density, confinement, rigidity, topography, and non-linear mechanics and their implications on tumor cell behavior. We also emphasize how perturbations in these cues alter cellular mechanisms of mechanotransduction, consequently enhancing malignancy. Finally, we elucidate engineering techniques to individually emulate the mechanical properties of tumors that could help serve as toolkits for developing and testing ECM-targeted therapeutics on novel bioengineered tumor platforms. STATEMENT OF SIGNIFICANCE: Disrupted ECM mechanics is a driving force for transitioning incipient cells to life-threatening malignant variants. Understanding these ECM changes can be crucial as they may aid in developing several efficacious drugs that not only focus on inducing cytotoxic effects but also target specific matrix mechanical cues that support and enhance tumor invasiveness. Designing and implementing an optimal tumor mimic can allow us to predictively map biophysical cue-modulated cell behaviors and facilitate the design of improved lab-grown tumor models with accurately controlled structural features. This review focuses on the abnormal changes within the ECM during tumorigenesis and its implications on tumor cell-matrix mechanoreciprocity. Additionally, it accentuates engineering approaches to produce ECM features of varying levels of complexity which is critical for improving the efficiency of current engineered tumor tissue models.

Establishment of decellularized extracellular matrix scaffold derived from caprine pancreas as a novel alternative template over porcine pancreatic scaffold for prospective biomedical application

In this study, the caprine pancreas has been presented as an alternative to the porcine organ for pancreatic xenotransplantation with lesser risk factors. The obtained caprine pancreas underwent a systematic cycle of detergent perfusion for decellularization. It was perfused using anionic (0.5% w/v sodium dodecyl sulfate) as well as non-ionic (0.1% v/v triton X-100, t-octyl phenoxy polyethoxy ethanol) detergents and washed intermittently with 1XPBS supplemented with 0.1% v/v antibiotic and nucleases in a gravitation-driven set-up. After 48 h, a white decellularized pancreas was obtained, and its extracellular matrix (ECM) content was examined for scaffold-like properties. The ECM content was assessed for removal of cellular content, and nuclear material was evaluated with temporal H&E staining. Quantified DNA was found to be present in a negligible amount in the resultant decellularized pancreas tissue (DPT), thus prohibiting it from triggering any immunogenicity. Collagen and fibronectin were confirmed to be preserved upon trichrome and immunohistochemical staining, respectively. SEM and AFM images reveal interconnected collagen fibril networks in the DPT, confirming that collagen was unaffected. sGAG was visualized using Prussian blue staining and quantified with DMMB assay, where DPT has effectively retained this ECM component. Uniaxial tensile analysis revealed that DPT possesses better elasticity than NPT (native pancreatic tissue). Physical parameters like tensile strength, stiffness, biodegradation, and swelling index were retained in the DPT with negligible loss. The cytocompatibility analysis of DPT has shown no cytotoxic effect for up to 72 h on normal insulin-producing cells (MIN-6) and cancerous glioblastoma (LN229) cells in vitro. The scaffold was recellularized using isolated mouse islets, which have established in vitro cell proliferation for up to 9 days. The scaffold received at the end of the decellularization cycle was found to be non-toxic to the cells, retained biological and physical properties of the native ECM, suitable for recellularization, and can be used as a safer and better alternative as a transplantable organ from a xenogeneic source.

Kinetic model description of dissipation and recovery in collagen fibrils under cyclic loading

Collagen fibrils, when subjected to cyclic loading, are known to exhibit hysteretic behavior with energy dissipation that is partially recovered on relaxation. In this paper, we develop a kinetic model for a collagen fibril incorporating presence of hidden loops and stochastic fragmentation as well as reformation of sacrificial bonds. We show that the model reproduces well the characteristic features of reported experimental data on cyclic response of collagen fibrils, such as moving hysteresis loops, time evolution of residual strains and energy dissipation, recovery on relaxation, etc. We show that the approach to the steady state is controlled by a characteristic cycle number for both residual strain as well as energy dissipation and is in good agreement with reported existing experimental data.

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach

Collagen is one of the most important structural proteins in biology, and its structural hierarchy plays a crucial role in many mechanically important biomaterials. Here, we demonstrate how transformer models can be used to predict, directly from the primary amino acid sequence, the thermal stability of collagen triple helices, measured via the melting temperature T_m. We report two distinct transformer architectures to compare performance. First, we train a small transformer model from scratch, using our collagen data set featuring only 633 sequence-to-T_m pairings. Second, we use a large pretrained transformer model, ProtBERT, and fine-tune it for a particular downstream task by utilizing sequence-to-T_m pairings, using a deep convolutional network to translate natural language processing BERT embeddings into required features. Both the small transformer model and the fine-tuned ProtBERT model have similar R² values of test data (R² = 0.84 vs 0.79, respectively), but the ProtBERT is a much larger pretrained model that may not always be applicable for other biological or biomaterials questions. Specifically, we show that the small transformer model requires only 0.026% of the number of parameters compared to the much larger model but reaches almost the same accuracy for the test set. We compare the performance of both models against 71 newly published sequences for which T_m has been obtained as a validation set and find reasonable agreement, with ProtBERT outperforming the small transformer model. The results presented here are, to our best knowledge, the first demonstration of the use of transformer models for relatively small data sets and for the prediction of specific biophysical properties of interest. We anticipate that the work presented here serves as a starting point for transformer models to be applied to other biophysical problems.

Jellyfish as Food: A Narrative Review

Studies toward a sustainable future conducted by international organizations uniformly agree about having to change some of our present consumer behaviors. Regarding food, suggestions include eating locally farmed, less industrialized and renewable food to promote health and circularity, and limiting waste. Jellyfish are frequently sorted and discarded after being caught with fish in fishing nets and gear. In contrast, we propose utilizing this by-catch as food. This review discusses the economic value and sustainability of jellyfish, the technologies used to prepare them for human consumption, their nutritional profile and health impacts and, finally, consumer acceptability and sensory evaluation of jellyfish food products. This discussion is critical for promoting jellyfish as an important aquatic resource to support blue and circular economies.

Probing the alignment-dependent mechanical behaviors and time-evolutional aligning process of collagen scaffolds

Efficiently manipulating and reproducing collagen (COL) alignment in vitro remains challenging because many of the fundamental mechanisms underlying and guiding the alignment process are not known. We reconcile experiments and coarse-grained molecular dynamics simulations to investigate the mechanical behaviors of a growing COL scaffold and assay how changes in fiber alignment and various cross-linking densities impact their alignment dynamics under shear flow. We find higher cross-link densities and alignment levels significantly enhance the apparent tensile/shear moduli and strength of a bulk COL system, suggesting potential measures to facilitate the design of stronger COL based materials. Since fibril alignment plays a key factor in scaffold mechanics, we next investigate the molecular mechanism behind fibril alignment with Couette flow by computationally investigating the effects of COL's structural properties such as chain lengths, number of chains, tethering conditions, and initial COL conformations on the COL's final alignment level. Our computations suggest that longer chain lengths, more chains, greater amounts of tethering, and initial anisotropic COL conformations benefit the final alignment, but the effect of chain lengths may be more dominant over other factors. These results provide important parameters for consideration in manufacturing COL-based scaffolds where alignment and cross-linking are necessary for regulating performance.

Understanding the inelastic response of collagen fibrils: A viscoelastic-plastic constitutive model

Collagen fibrils, which are the lowest level fibrillar unit of organization of collagen, are thus of primary interest towards understanding the mechanical behavior of load-bearing soft tissues. The deformation of collagen fibrils shows unique mechanical features; namely, their high energy dissipation is even superior compared to most engineering materials. Additionally, there are indications that cyclic loading can further improve the toughness of collagen fibrils. Recent experiments from Liu at al. (2018) focused on the response of type I collagen fibrils to uniaxial cyclic loading, revealing some interesting results regarding their rate-dependent and inelastic response. In this work, we aim to develop a model that allows interpreting the complex nonlinear and inelastic response of collagen fibrils under cyclic loading. We propose a constitutive model that accounts for viscoelastic deformations through a decoupled strain-energy density function (into an elastic and a viscous parts), and for plastic deformations through plastic evolution laws. The stress-stretch response results obtained using this constitutive law showed good agreement with experimental data over complex loading paths. Ultimately we use the model to gain more insights on how cyclic loading and rate effects control the interplay between viscoelastic and plastic deformation in collagen fibrils, and to extrapolate the results from experimental data, analyzing how complex cyclic load influences energy dissipation and deformation mechanisms. STATEMENT OF SIGNIFICANCE: In this work, we develop a viscoelastic-plastic constitutive model for collagen fibrils with the aim of analyzing the effects of inelasticity and energy dissipation in this material, and more specifically the competition between viscoelasticity and plasticity in the context of cyclic loading and overload. Experimental and theoretical approaches so far have not fully clarified the interplay between viscous and plastic deformations during cyclic loading of collagen fibrils. Here, we aim to interpret the complex nonlinear response of collagen fibrils and, ultimately, suggest predictive capabilities that can inform tissue-level response and injury. To validate our model, we compare our results against the stress-stretch data obtained from experiments of cyclic loaded single fibrils performed by Liu et al. (2018).

Electrospun Scaffolds as Cell Culture Substrates for the Cultivation of an In Vitro Blood-Brain Barrier Model Using Human Induced Pluripotent Stem Cells

The human blood–brain barrier (BBB) represents the interface of microvasculature and the central nervous system, regulating the transport of nutrients and protecting the brain from external threats. To gain a deeper understanding of (patho)physiological processes affecting the BBB, sophisticated models mimicking the in vivo situation are required. Currently, most in vitro models are cultivated on stiff, semipermeable, and non-biodegradable Transwell^® membrane inserts, not adequately mimicking the complexity of the extracellular environment of the native human BBB. To overcome these disadvantages, we developed three-dimensional electrospun scaffolds resembling the natural structure of the human extracellular matrix. The polymer fibers of the scaffold imitate collagen fibrils of the human basement membrane, exhibiting excellent wettability and biomechanical properties, thus facilitating cell adhesion, proliferation, and migration. Cultivation of human induced pluripotent stem cells (hiPSCs) on these scaffolds enabled the development of a physiological BBB phenotype monitored via the formation of tight junctions and validated by the paracellular permeability of sodium fluorescein, further accentuating the non-linearity of TEER and barrier permeability. The novel in vitro model of the BBB forms a tight endothelial barrier, offering a platform to study barrier functions in a (patho)physiologically relevant context.

The Influence of the Structure of Selected Polymers on Their Properties and Food-Related Applications

Every application of a substance results from the macroscopic property of the substance that is related to the substance’s microscopic structure. For example, the forged park gate in your city was produced thanks to the malleability and ductility of metals, which are related to the ability of shifting of layers of metal cations, while fire extinguishing powders use the high boiling point of compounds related to their regular ionic and covalent structures. This also applies to polymers. The purpose of this review is to summarise and present information on selected food-related biopolymers, with special attention on their respective structures, related properties, and resultant applications. Moreover, this paper also highlights how the treatment method used affects the structure, properties, and, hence, applications of some polysaccharides. Despite a strong focus on food-related biopolymers, this review is addressed to a broad community of both material engineers and food researchers.

Nanoarchitectonics for Ultrathin Gold Films Deposited on Collagen Fabric by High-Power Impulse Magnetron Sputtering

Gold nanoparticles conjugated with collagen molecules and fibers have been proven to improve structure strength, water and enzyme degradation resistance, cell attachment, cell proliferation, and skin wound healing. In this study, high-power impulse magnetron sputtering (HiPIMS) was used to deposit ultrathin gold films (UTGF) and discontinuous island structures on type I collagen substrates. A long turn-off time of duty cycle and low chamber temperature of HiPIMS maintained substrate morphology. Increasing the deposition time from 6 s to 30 s elevated the substrate surface coverage by UTGF up to 91.79%, as observed by a field emission scanning electron microscope. X-ray diffractometry analysis revealed signature low and wide peaks for Au (111). The important surface functional groups and signature peaks of collagen substrate remained unchanged according to Fourier transform infrared spectroscopy results. Multi-peak curve fitting of the Amide I spectrum revealed the non-changed protein secondary structure of type I collagen, which mainly consists of α-helix. Atomic force microscopy observation showed that the roughness average value shifted from 1.74 to 4.17 nm by increasing the deposition time from 13 s to 77 s. The uneven surface of collagen substrate made quantification of thin film thickness by AFM difficult. Instead, UTGF thickness was measured using simultaneously deposited glass specimens placed in an HiPIMS chamber with collagen substrates. Film thickness was 3.99 and 10.37 nm at deposition times of 13 and 77 s, respectively. X-ray photoelectron spectroscopy showed preserved substrate elements on the surface. Surface water contact angle measurement revealed the same temporary hydrophobic behavior before water absorption via exposed collagen substrates, regardless of deposition time. In conclusion, HiPIMS is an effective method to deposit UTGF on biomedical materials such as collagen without damaging valuable substrates. The composition of two materials could be further used for biomedical purposes with preserved functions of UTGF and collagen.

Multiscale Characterization of Type I Collagen Fibril Stress–Strain Behavior under Tensile Load: Analytical vs. MD Approaches

Type I collagen is one of the most important proteins in the human body because of its role in providing structural support to the extracellular matrix of the connective tissues. Understanding its mechanical properties was widely investigated using experimental testing as well as molecular and finite element simulations. In this work, we present a new approach for defining the properties of the type I collagen fibrils by analytically formulating its response when subjected to a tensile load and investigating the effects of enzymatic crosslinks on the behavioral response. We reveal some of the shortcomings of the molecular dynamics (MD) method and how they affect the obtained stress–strain behavior of the fibril, and we prove that not only does MD underestimate the Young’s modulus and the ultimate tensile strength of the collagen fibrils, but also fails to detect the mechanics of some stretching phases of the fibril. We prove that non-crosslinked fibrils have three tension phases: (i) an initial elastic deformation corresponding to the collagen molecule uncoiling, (ii) a linear regime related to the stretching of the backbone of the tropocollagen molecules, and (iii) a plastic regime dominated by molecular sliding. We also show that for crosslinked fibrils, the second regime can be subdivided into three sub-regimes, and we define the properties of each regime. We also prove, analytically, the alleged MD quadratic relation between the ultimate tensile strength of the fibril and the concentration of enzymatic crosslinks (β).

Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: a coarse-grained molecular dynamics simulation study

Collagen-like peptides (CLP) are multifunctional materials garnering a lot of recent interest from the biomaterials community due to their hierarchical assembly and tunable physicochemical properties. In this work, we present a computational study that links the design of CLP heterotrimers to the thermal stability of the triple helix and their self-assembly into fibrillar aggregates and percolated networks. Unlike homotrimeric helices, the CLP heterotrimeric triple helices in this study are made of CLP strands of different chain lengths that result in 'sticky' ends with available hydrogen bonding groups. These 'sticky' ends at one end or both ends of the CLP heterotrimer then facilitate inter-helix hydrogen bonding leading to self-assembly into fibrils (clusters) and percolated networks. We consider the cases of three sticky end lengths - two, four, and six repeat units - present entirely on one end or split between two ends of the CLP heterotrimer. We observe in CLP heterotrimer melting curves generated using coarse grained Langevin dynamics simulations at low CLP concentration that increasing sticky end length results in lower melting temperatures for both one and two sticky ended CLP designs. At higher CLP concentrations, we observe non-monotonic trends in cluster sizes with increasing sticky end length with one sticky end but not for two sticky ends with the same number of available hydrogen bonding groups as the one sticky end; this nonmonotonicity stems from the formation of turn structures stabilized by hydrogen bonds at the single, sticky end for sticky end lengths greater than four repeat units. With increasing CLP concentration, heterotrimers also form percolated networks with increasing sticky end length with a minimum sticky end length of four repeat units required to observe percolation. Overall, this work informs the design of thermoresponsive, peptide-based biomaterials with desired morphologies using strand length and dispersity as a handle for tuning thermal stability and formation of supramolecular structures.

Tropocollagen springs allow collagen fibrils to stretch elastically

The mechanical properties of connective tissues are tailored to their specific function, and changes can lead to dysfunction and pathology. In most mammalian tissues the mechanical environment is governed by the micro- and nano-scale structure of collagen and its interaction with other tissue components, however these hierarchical properties remain poorly understood. In this study we use the human cornea as a model system to characterise and quantify the dominant deformation mechanisms of connective tissue in response to cyclic loads of physiological magnitude. Synchronised biomechanical testing, x-ray scattering and 3D digital image correlation revealed the presence of two dominant mechanisms: collagen fibril elongation due to a largely elastic, spring-like straightening of tropocollagen supramolecular twist, and a more viscous straightening of fibril crimp that gradually increased over successive loading cycles. The distinct mechanical properties of the two mechanisms suggest they have separate roles in vivo. The elastic, spring-like mechanism is fast-acting and likely responds to stresses associated with the cardiac cycle, while the more viscous crimp mechanism will respond to slower processes, such as postural stresses. It is anticipated that these findings will have broad applicability to understanding the normal and pathological functioning of other connective tissues such as skin and blood vessels that exhibit both helical structures and crimp.

Statement of significance

The tropocollagen spring mechanism allows collagen fibrils from some tissues to elongate significantly under small loads, and its recent discovery has the potential to change our fundamental understanding of how tissue deforms. This time-resolved study quantifies the contribution of the spring mechanism to the local strain in stretched tissue and compares it to the contribution associated with the straightening of fibril waviness, the widely accepted primary low-load strain mechanism. The spring mechanism contributed more to the local tissue strain than fibril straightening, and was found to be elastic while fibril straightening was more viscous. The results suggest that the viscoelastic behaviour of a biomaterial is controlled, at least in part, by the relative amount of fibril-scale crimp and tropocollagen supramolecular twist.

Acquiring structural and mechanical information of a fibrous network through deep learning

Fibrous networks play an essential role in the structure and properties of a variety of biological and engineered materials, such as cytoskeletons, protein filament-based hydrogels, and entangled or crosslinked polymer chains. Therefore, insight into the structural features of these fibrous networks and their constituent filaments is critical for discovering the structure-property-function relationships of these material systems. In this paper, a fibrous network-deep learning system (FN-DLS) is established to extract fibrous network structure information from atomic force microscopy images. FN-DLS accurately assesses the structural and mechanical characteristics of fibrous networks, such as contour length, number of nodes, persistence length, mesh size and fractal dimension. As an open-source system, FN-DLS is expected to serve a vast community of scientists working on very diverse disciplines and pave the way for new approaches on the study of biological and synthetic polymer and filament networks found in current applied and fundamental sciences.

Recent strategies of collagen-based biomaterials for cartilage repair: from structure cognition to function endowment

Collagen, characteristic in biomimetic composition and hierarchical structure, boasts a huge potential in repairing cartilage defect due to its extraordinary bioactivities and regulated physicochemical properties, such as low immunogenicity, biocompatibility and controllable degradation, which promotes the cell adhesion, migration and proliferation. Therefore, collagen-based biomaterial has been explored as porous scaffolds or functional coatings in cell-free scaffold and tissue engineering strategy for cartilage repairing. Among those forming technologies, freeze-dry is frequently used with special modifications while 3D-printing and electrospinning serve as the structure-controller in a more precise way. Besides, appropriate cross-linking treatment and incorporation with bioactive substance generally help the collagen-based biomaterials to meet the physicochemical requirement in the defect site and strengthen the repairing performance. Furthermore, comprehensive evaluations on the repair effects of biomaterials are sorted out in terms of in vitro, in vivo and clinical assessments, focusing on the morphology observation, characteristic production and critical gene expression. Finally, the challenge of biomaterial-based therapy for cartilage defect repairing was summarized, which is, the adaption to the highly complex structure and functional difference of cartilage.

Graphical abstract

Effect of Dialdehyde Carboxymethyl Cellulose Cross-Linking on the Porous Structure of the Collagen Matrix

Porous structures are essential for some collagen-based biomaterials and can be regulated by crosslinkers. Herein, dialdehyde carboxymethyl cellulose (DCMC) crosslinkers with similar size but different aldehyde group contents were prepared through periodate oxidation of sodium carboxymethyl cellulose with varying degrees of substitution (DS). They can penetrate into the hierarchy of fibril and form inter-molecular and intra-fibril cross-linking within the collagen matrix due to their nanoscale sizes and reactive aldehyde groups. The collagen matrices possessed higher porosity, significantly greater proportion of large pores (Φ > 10 μm), and shorter D-periodicity after cross-linking, showing greater potential for biomedical applications. In addition, the crosslinked collagen matrices showed satisfactory biocompatibility and biodegradation. The decreased DS of carboxymethyl cellulose, which led to the increased aldehyde content of corresponding DCMC, brought about an enhanced cross-linking degree, porosity, and proportion of large pores of the crosslinked collagen matrix. DCMC dosage of 6% was sufficient for cross-linking and pore formation. Excess DCMC would physically deposit in the matrix and decrease the porosity instead. Therefore, the desired pore properties of the collagen matrix could be obtained by regulating the structure of DCMC and thereby achieving the required functions of the biomaterial.

Strain rate induced toughening of individual collagen fibrils

The nonlinear mechanical behavior of individual nanoscale collagen fibrils is governed by molecular stretching and sliding that result in a viscous response, which is still not fully understood. Toward this goal, the in vitro mechanical behavior of individual reconstituted mammalian collagen fibrils was quantified in a broad range of strain-rates, spanning roughly six orders of magnitude, from 10^-4 to 35 s^-1. It is shown that the nonlinear mechanical response is strain rate sensitive with the tangent modulus in the linear deformation regime increasing monotonically from 214 ± 8 to 358 ± 11 MPa. More pronounced is the effect of the strain rate on the ultimate tensile strength that is found to increase monotonically by a factor of four, from 42 ± 6 to 160 ± 14 MPa. Importantly, fibril strengthening takes place without a reduction in ductility, which results in equivalently large increase in toughness with the increasing strain rate. This experimental strain rate dependent mechanical response is captured well by a structural constitutive model that incorporates the salient features of the collagen microstructure via a process of gradual recruitment of kinked tropocollagen molecules, thus giving rise to the initial "toe-heel" mechanical behavior, followed by molecular stretching and sustained intermolecular slip that is initiated at a strain rate dependent stress threshold. The model shows that the fraction of tropocollagen molecules undergoing straightening increases continuously during loading, whereas molecular sliding is initiated after a small fibril strain (1%-2%) and progressively increases with applied strain.

Biomaterials via peptide assembly: Design, characterization, and application in tissue engineering

A core challenge in biomaterials, with both fundamental significance and technological relevance, concerns the rational design of bioactive microenvironments. Designed properly, peptides can undergo supramolecular assembly into dynamic, physical hydrogels that mimic the mechanical, topological, and biochemical features of native tissue microenvironments. The relatively facile, inexpensive, and automatable preparation of peptides, coupled with low batch-to-batch variability, motivates the expanded use of assembling peptide hydrogels for biomedical applications. Integral to realizing dynamic peptide assemblies as functional biomaterials for tissue engineering is an understanding of the molecular and macroscopic features that govern assembly, morphology, and biological interactions. In this review, we first discuss the design of assembling peptides, including primary structure (sequence), secondary structure (e.g., α-helix and β-sheets), and molecular interactions that facilitate assembly into multiscale materials with desired properties. Next, we describe characterization tools for elucidating molecular structure and interactions, morphology, bulk properties, and biological functionality. Understanding of these characterization methods enables researchers to access a variety of approaches in this ever-expanding field. Finally, we discuss the biological properties and applications of peptide-based biomaterials for engineering several important tissues. By connecting molecular features and mechanisms of assembling peptides to the material and biological properties, we aim to guide the design and characterization of peptide-based biomaterials for tissue engineering and regenerative medicine. STATEMENT OF SIGNIFICANCE: Engineering peptide-based biomaterials that mimic the topological and mechanical properties of natural extracellular matrices provide excellent opportunities to direct cell behavior for regenerative medicine and tissue engineering. Here we review the molecular-scale features of assembling peptides that result in biomaterials that exhibit a variety of relevant extracellular matrix-mimetic properties and promote beneficial cell-biomaterial interactions. Aiming to inspire and guide researchers approaching this challenge from both the peptide biomaterial design and tissue engineering perspectives, we also present characterization tools for understanding the connection between peptide structure and properties and highlight the use of peptide-based biomaterials in neural, orthopedic, cardiac, muscular, and immune engineering applications.

Study on fracture behavior of molars based on three-dimensional high-precision computerized tomography scanning and numerical simulation

A series of three-dimensional (3D) numerical simulations are conducted to investigate the gradual failure process of molars in this study. The real morphology and internal mesoscopic structure of a whole tooth are implemented into the numerical simulations through computerized tomography scanning, digital image processing, and 3D matrix mapping. The failure process of the whole tooth subject to compressions including crack initiation, crack propagation, and final failure pattern is reproduced using 3D realistic failure process analysis (RFPA3D) method. It is concluded that a series of microcracks are gradually initiated, nucleated, and subsequently interconnect to form macroscopic cracks when the teeth are under over-compressions. The propagation of the macroscopic cracks results in the formation of fracture surfaces and penetrating cracks, which are essential signs and manifestations of the tooth failure. Moreover, the simulations reveal that, the material heterogeneity is a critical factor that affects the mechanical properties and fracture modes of the teeth, which vary from crown fractures to crown-root fractures and root fractures depending on different homogeneity indices.

Simulation of defects, flexibility and rupture in biopolymer networks

Networks of biopolymers occur often in nature, and are vulnerable to damage over time. In this work, a coarse grained model of collagen IV molecules is applied in a 2D hexagonal network and the mechanisms by which these networks can rupture are explored. The networks are stretched linearly in order to study their structural limits and mechanism of rupture over timescale of up to 100 μs. Metrics are developed to track the damage networks suffer over time, and qualitatively analyse ruptures that occur. Further simulations repeatedly stretch the networks sinusoidally to mimic the in vivo strains. Defects of increasing levels of complexity are introduced into an ordered network, and their effect on the rupturing behaviour of the biopolymer networks studied. The effect of introducing holes of varying size in the network, as well as strips of finite width to mimic surgical damage are studied. These demonstrate the importance of the flexibility of the networks to preventing damage.

Stiffness Variation of 3D Collagen Networks by Surface Functionalization of Network Fibrils with Sulfonated Polymers

Fibrillar collagen is the most prominent protein in the mammalian extracellular matrix. Therefore, it is also widely used for cell culture research and clinical therapy as a biomimetic 3D scaffold. Charged biopolymers, such as sulfated glycosaminoglycans, occur in vivo in close contact with collagen fibrils, affecting many functional properties such as mechanics and binding of growth factors. For in vitro application, the functions of sulfated biopolymer decorations of fibrillar collagen materials are hardly understood. Herein, we report new results on the stiffness dependence of 3D collagen I networks by surface functionalization of the network fibrils with synthetic sulfonated polymers, namely, poly(styrene sulfonate) (PSS) and poly(vinyl sulfonate) (PVS). A non-monotonic stiffness dependence on the amount of adsorbed polymer was found for both polymers. The stiffness dependence correlated to a transition from mono- to multilayer adsorption of sulfonated polymers on the fibrils, which was most prominent for PVS. PVS mono- and multilayers caused a network stiffness change by a factor of 0.3 and 2, respectively. A charge-dependent weakening of intrafibrillar salt bridges by the adsorbed sulfonated polymers leading to fibrillar softening is discussed as the mechanism for the stiffness decrease in the monolayer regime. In contrast, multilayer adsorption can be assumed to induce interfibrillar bridging and an increase in network stiffness. Our in vitro results have a strong implication on in vivo characteristics of fibrillar collagen I, as sulfated glycosaminoglycans frequently attach to collagen fibrils in various tissues, calling for an up to now overlooked impact on matrix and tendon mechanics.

Graphene-Lined Porous Gelatin Glycidyl Methacrylate Hydrogels: Implications for Tissue Engineering

Despite rigorous research, inferior mechanical properties and structural homogeneity are the main challenges constraining hydrogel's suturability to host tissue and limiting its clinical applications. To tackle those, we developed a reverse solvent interface trapping method, in which organized, graphene-coated microspherical cavities were introduced into a hydrogel to create heterogeneity and make it suturable. To generate those cavities, (i) graphite exfoliates to graphene sheets, which spread at the water/ heptane interfaces of the microemulsion, (ii) heptane fills the microspheres coated by graphene, and (iii) a cross-linkable hydrogel dissolved in water fills the voids. Cross-linking solidifies such microemulsion to a strong, suturable, permanent hybrid architecture, which has better mechanical properties, yet it is biocompatible and supports cell adhesion and proliferation. These properties along with the ease and biosafety of fabrication suggest the potential of this strategy to enhance tissue engineering outcomes by generating various suturable scaffolds for biomedical applications, such as donor cornea carriers for Boston keratoprosthesis (BK).

ColGen: An end-to-end deep learning model to predict thermal stability of de novo collagen sequences

Collagen is the most abundant structural protein in humans, with dozens of sequence variants accounting for over 30% of the protein in an animal body. The fibrillar and hierarchical arrangements of collagen are critical in providing mechanical properties with high strength and toughness. Due to this ubiquitous role in human tissues, collagen-based biomaterials are commonly used for tissue repairs and regeneration, requiring chemical and thermal stability over a range of temperatures during materials preparation ex vivo and subsequent utility in vivo. Collagen unfolds from a triple helix to a random coil structure during a temperature interval in which the midpoint or T_m is used as a measure to evaluate the thermal stability of the molecules. However, finding a robust framework to facilitate the design of a specific collagen sequence to yield a specific T_m remains a challenge, including using conventional molecular dynamics modeling. Here we propose a de novo framework to provide a model that outputs the T_m values of input collagen sequences by incorporating deep learning trained on a large data set of collagen sequences and corresponding T_m values. By using this framework, we are able to quickly evaluate how mutations and order in the primary sequence affect the stability of collagen triple helices. Specifically, we confirm that mutations to glycines, mutations in the middle of a sequence, and short sequence lengths cause the greatest drop in T_m values.

Intermediate Structural Hierarchy in Biological Networks Modulates the Fractal Dimension and Force Distribution of Percolating Clusters

Globular protein hydrogels are an emerging class of materials with the potential for rational design, and a generalized understanding of how their network properties emerge from the structure and dynamics of the building block is a key challenge. Here we computationally investigate the effect of intermediate (polymeric) nanoscale structure on the formation of protein hydrogels. We show that changes in both the cross-link topology and flexibility of the polymeric building block lead to changes in the force transmission around the system and provide insight into the dynamic network formation processes. The preassembled intermediate structure provides a novel structural coordinate for the hierarchical modulation of macroscopic network properties, as well as furthering our understanding of the general dynamics of network formation.

An AFM study of the nanostructural response of New Zealand white rabbit Achilles tendons to cyclic loading

The nanostructural response of New Zealand white rabbit Achilles tendons to a fatigue damage model was assessed quantitatively and qualitatively using the endpoint of dose assessments of each tendon from our previous study. The change in mechanical properties was assessed concurrently with nanostructural change in the same non-viable intact tendon. Atomic force microscopy was used to study the elongation of D-periodicities, and the changes were compared both within the same fibril bundle and between fibril bundles. D-periodicities increased due to both increased strain and increasing numbers of fatigue cycles. Although no significant difference in D-periodicity lengthening was found between fibril bundles, the lengthening of D-periodicity correlated strongly with the overall tendon mechanical changes. The accurate quantification of fibril elongation in response to macroscopic applied strain assisted in assessing the complex structure-function relationship in Achilles tendons.

The Effect of Enzymatic Crosslink Degradation on the Mechanics of the Anterior Cruciate Ligament: A Hybrid Multi-Domain Model

The anterior cruciate ligament’s (ACL) mechanics is an important factor governing the ligament’s integrity and, hence, the knee joint’s response. Despite many investigations in this area, the cause and effect of injuries remain unclear or unknown. This may be due to the complexity of the direct link between macro- and micro-scale damage mechanisms. In the first part of this investigation, a three-dimensional coarse-grained model of collagen fibril (type I) was developed using a bottom-up approach to investigate deformation mechanisms under tensile testing. The output of this molecular level was used later to calibrate the parameters of a hierarchical multi-scale fibril-reinforced hyper-elastoplastic model of the ACL. Our model enabled us to determine the mechanical behavior of the ACL as a function of the basic response of the collagen molecules. Modeled elastic response and damage distribution were in good agreement with the reported measurements and computational investigations. Our results suggest that degradation of crosslink content dictates the loss of the stiffness of the fibrils and, hence, damage to the ACL. Therefore, the proposed computational frame is a promising tool that will allow new insights into the biomechanics of the ACL.