Quasi-hexagonal molecular packing in collagen fibrils

The action of microbial collagenases in dentinal matrix degradation in root caries and potential strategies for its management: a comprehensive state-of-the-art review

Conventional views associate microbial biofilm with demineralization in root caries (RC) onset, while research on their collagenases role in the breakdown of collagen matrix has been sporadically developed, primarily in vitro. Recent discoveries, however, reveal proteolytic bacteria enrichment, specially Porphyromonas and other periodontitis-associated bacteria in subgingivally extended lesions, suggesting a potential role in RC by the catabolism of dentin organic matrix. Moreover, genes encoding proteases and bacterial collagenases, including the U32 family collagenases, were found to be overexpressed in both coronal and root dentinal caries. Despite these advancements, to prove microbial collagenolytic proteases' definitive role in RC remains a significant challenge. A more thorough investigation is warranted to explore the potential of anti-collagenolytic agents in modulating biofilm metabolic processes or inhibiting/reducing the size of RC lesions. Prospective treatments targeting collagenases and promoting biomodification through collagen fibril cross-linking show promise for RC prevention and management. However, these studies are currently in the in vitro phase, necessitating additional research to translate findings into clinical applications. This is a comprehensive state-of-the-art review aimed to explore contributing factors to the formation of RC lesions, particularly focusing on collagen degradation in root tissues by microbial collagenases.

Single-Crystal-to-Single-Crystal Topochemical Synthesis of a Collagen-inspired Covalent Helical Polymer

There is much demand for crystalline covalent helical polymers. Inspired by the helical structure of collagen, we synthesized a covalent helical polymer wherein the repeating dipeptide Gly-Pro units are connected by triazole linkages. We synthesized an azide and alkyne-modified dipeptide monomer made up of the repeating amino acid sequence of collagen. In its crystals, the monomer molecules aligned in head-to-tail fashion with proximally placed azide and alkyne forming supramolecular helices. At 60 °C, the monomer underwent single-crystal-to-single-crystal (SCSC) topochemical azide-alkyne cycloaddition polymerization, yielding a covalent helical polymer as confirmed by single-crystal X-ray diffraction (SCXRD) analysis. Compared to the monomer crystals, the polymer single-crystals were very strong and showed three-fold increase in Young's modulus, which is higher than collagen, many synthetic polymers and other materials. The crystals of this covalent helical polymer could bear loads as high as 1.5 million times of their own weight without deformation. These crystals could also withstand high compression force and did not disintegrate even at an applied force of 98 kN. Such light-weight strong materials are in demand for various technological applications.

What are the key mechanical mechanisms governing integrin-mediated cell migration in three-dimensional fiber networks?

Cell migration plays a vital role in numerous processes such as development, wound healing, or cancer. It is well known that numerous complex mechanisms are involved in cell migration. However, so far it remains poorly understood what are the key mechanisms required to produce the main characteristics of this behavior. The reason is a methodological one. In experimental studies, specific factors and mechanisms can be promoted or inhibited. However, while doing so, there can always be others in the background which play key roles but which have simply remained unattended so far. This makes it very difficult to validate any hypothesis about a minimal set of factors and mechanisms required to produce cell migration. To overcome this natural limitation of experimental studies, we developed a computational model where cells and extracellular matrix fibers are represented by discrete mechanical objects on the micrometer scale. In this model, we had exact control of the mechanisms by which cells and matrix fibers interacted with each other. This enabled us to identify the key mechanisms required to produce physiologically realistic cell migration (including advanced phenomena such as durotaxis and a biphasic relation between migration efficiency and matrix stiffness). We found that two main mechanisms are required to this end: a catch-slip bond of individual integrins and cytoskeletal actin-myosin contraction. Notably, more advanced phenomena such as cell polarization or details of mechanosensing were not necessary to qualitatively reproduce the main characteristics of cell migration observed in experiments.

Role of carboxylic organic molecules in interfibrillar collagen mineralization

Bone is a composite material made up of inorganic and organic counterparts. Most of the inorganic counterpart accounts for calcium phosphate (CaP) whereas the major organic part is composed of collagen. The interfibrillar mineralization of collagen is an important step in the biomineralization of bone and tooth. Studies have shown that synthetic CaP undergoes auto-transformation to apatite nanocrystals before entering the gap zone of collagen. Also, the synthetic amorphous calcium phosphate/collagen combination alone is not capable of initiating apatite nucleation rapidly. Therefore, it was understood that there is the presence of a nucleation catalyst obstructing the auto-transformation of CaP before entering the collagen gap zone and initiating rapid nucleation after entering the collagen gap zone. Therefore, studies were focused on finding the nucleation catalyst responsible for the regulation of interfibrillar collagen mineralization. Organic macromolecules and low-molecular-weight carboxylic compounds are predominantly present in the bone and tooth. These organic compounds can interact with both apatite and collagen. Adsorption of the organic compounds on the apatite nanocrystal governs the nucleation, crystal growth, lattice orientation, particle size, and distribution. Additionally, they prevent the auto-transformation of CaP into apatite before entering the interfibrillar compartment of the collagen fibril. Therefore, many carboxylic organic compounds have been utilized in developing CaP. In this review, we have covered different carboxylate organic compounds governing collagen interfibrillar mineralization.

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.

Biomaterial functionalization with triple-helical peptides for tissue engineering

In the growing field of tissue engineering, providing cells in biomaterials with the adequate biological cues represents an increasingly important challenge. Yet, biomaterials with excellent mechanical properties often are often biologically inert to many cell types. To address this issue, researchers resort to functionalization, i.e. the surface modification of a biomaterial with active molecules or substances. Functionalization notably aims to replicate the native cellular microenvironment provided by the extracellular matrix, and in particular by collagen, its major component. As our understanding of biological processes regulating cell behaviour increases, functionalization with biomolecules binding cell surface receptors constitutes a promising strategy. Amongst these, triple-helical peptides (THPs) that reproduce the architectural and biological properties of collagen are especially attractive. Indeed, THPs containing binding sites from the native collagen sequence have successfully been used to guide cell response by establishing cell-biomaterial interactions. Notably, the GFOGER motif recognising the collagen-binding integrins is extensively employed as a cell adhesive peptide. In biomaterials, THPs efficiently improved cell adhesion, differentiation and function on biomaterials designed for tissue repair (especially for bone, cartilage, tendon and heart), vascular graft fabrication, wound dressing, drug delivery or immunomodulation. This review describes the key characteristics of THPs, their effect on cells when combined to biomaterials and their strong potential as biomimetic tools for regenerative medicine. STATEMENT OF SIGNIFICANCE: This review article describes how triple-helical peptides constitute efficient tools to improve cell-biomaterial interactions in tissue engineering. Triple helical peptides are bioactive molecules that mimic the architectural and biological properties of collagen. They have been successfully used to specifically recognize cell-surface receptors and provide cells seeded on biomaterials with controlled biological cues. Functionalization with triple-helical peptides has enabled researchers to improve cell function for regenerative medicine applications, such as tissue repair. However, despite encouraging results, this approach remains limited and under-exploited, and most functionalization strategies reported in the literature rely on biomolecules that are unable to address collagen-binding receptors. This review will assist researchers in selecting the correct tools to functionalize biomaterials in efforts to guide cellular response.

Collagen fibril formation in vitro: From origin to opportunities

Sometimes, to move forward, it is necessary to look back. Collagen type I is one of the most commonly used biomaterials in tissue engineering and regenerative medicine. There are a variety of collagen scaffolds and biomedical products based on collagen have been made, and the development of new ones is still ongoing. Materials, where collagen is in the fibrillar form, have some advantages: they have superior mechanical properties, higher degradation time and, what is most important, mimic the structure of the native extracellular matrix. There are some standard protocols for the formation of collagen fibrils in vitro, but if we look more carefully at those methods, we can see some controversies. For example, why is the formation of collagen gel commonly carried out at 37 ​°C, when it was well investigated that the temperature higher than 35 ​°C results in a formation of not well-ordered fibrils? Biomimetic collagen materials can be obtained both using culture medium or neutralizing solution, but it requires a deep understanding of all of the crucial points. One of this point is collagen extraction method, since not every method retains the ability of collagen to reconstitute native banded fibrils. Collagen polymorphism is also often overlooked in spite of the appearance of different polymorphic forms during fibril formation is possible, especially when collagen blends are utilized. In this review, we will not only pay attention to these issues, but we will overview the most prominent works related to the formation of collagen fibrils in vitro starting from the first approaches and moving to the up-to-date recipes.

Hierarchical organization of bone in three dimensions: A twist of twists

Structural hierarchy of bone - observed across multiple scales and in three dimensions (3D) - is essential to its mechanical performance. While the mineralized extracellular matrix of bone consists predominantly of carbonate-substituted hydroxyapatite, type I collagen fibrils, water, and noncollagenous organic constituents (mainly proteins and small proteoglycans), it is largely the 3D arrangement of these inorganic and organic constituents at each length scale that endow bone with its exceptional mechanical properties. Focusing on recent volumetric imaging studies of bone at each of these scales - from the level of individual mineralized collagen fibrils to that of whole bones - this graphical review builds upon and re-emphasizes the original work of James Bell Pettigrew and D'Arcy Thompson who first described the ubiquity of spiral structure in Nature. Here we illustrate and discuss the omnipresence of twisted, curved, sinusoidal, coiled, spiraling, and braided motifs in bone in at least nine of its twelve hierarchical levels - a visualization undertaking that has not been possible until recently with advances in 3D imaging technologies (previous 2D imaging does not provide this information). From this perspective, we hypothesize that the twisting motif occurring across each hierarchical level of bone is directly linked to enhancement of function, rather than being simply an energetically favorable way to assemble mineralized matrix components. We propose that attentive consideration of twists in bone and the skeleton at different scales will likely develop, and will enhance our understanding of structure-function relationships in bone.

Contrasting Local and Macroscopic Effects of Collagen Hydroxylation

Collagen is heavily hydroxylated. Experiments show that proline hydroxylation is important to triple helix (monomer) stability, fibril assembly, and interaction of fibrils with other molecules. Nevertheless, experiments also show that even without hydroxylation, type I collagen does assemble into its native D-banded fibrillar structure. This raises two questions. Firstly, even though hydroxylation removal marginally affects macroscopic structure, how does such an extensive chemical change, which is expected to substantially reduce hydrogen bonding capacity, affect local structure? Secondly, how does such a chemical perturbation, which is expected to substantially decrease electrostatic attraction between monomers, affect collagen's mechanical properties? To address these issues, we conduct a benchmarked molecular dynamics study of rat type I fibrils in the presence and absence of hydroxylation. Our simulations reproduce the experimental observation that hydroxylation removal has a minimal effect on collagen's D-band length. We also find that the gap-overlap ratio, monomer width and monomer length are minimally affected. Surprisingly, we find that de-hydroxylation also has a minor effect on the fibril's Young's modulus, and elastic stress build up is also accompanied by tightening of triple-helix windings. In terms of local structure, de-hydroxylation does result in a substantial drop (23%) in inter-monomer hydrogen bonding. However, at the same time, the local structures and inter-monomer hydrogen bonding networks of non-hydroxylated amino acids are also affected. It seems that it is this intrinsic plasticity in inter-monomer interactions that preclude fibrils from undergoing any large changes in macroscopic properties. Nevertheless, changes in local structure can be expected to directly impact collagen's interaction with extra-cellular matrix proteins. In general, this study highlights a key challenge in tissue engineering and medicine related to mapping collagen chemistry to macroscopic properties but suggests a path forward to address it using molecular dynamics simulations.

A computational framework for modeling cell-matrix interactions in soft biological tissues

Living soft tissues appear to promote the development and maintenance of a preferred mechanical state within a defined tolerance around a so-called set point. This phenomenon is often referred to as mechanical homeostasis. In contradiction to the prominent role of mechanical homeostasis in various (patho)physiological processes, its underlying micromechanical mechanisms acting on the level of individual cells and fibers remain poorly understood, especially how these mechanisms on the microscale lead to what we macroscopically call mechanical homeostasis. Here, we present a novel computational framework based on the finite element method that is constructed bottom up, that is, it models key mechanobiological mechanisms such as actin cytoskeleton contraction and molecular clutch behavior of individual cells interacting with a reconstructed three-dimensional extracellular fiber matrix. The framework reproduces many experimental observations regarding mechanical homeostasis on short time scales (hours), in which the deposition and degradation of extracellular matrix can largely be neglected. This model can serve as a systematic tool for future in silico studies of the origin of the numerous still unexplained experimental observations about mechanical homeostasis.

In Vitro Mineralization of Collagen

Collagen mineralization is a biological process in many skeletal elements in the animal kingdom. Examples of these collagen-based skeletons are the siliceous spicules of glass sponges or the intrafibrillar hydroxyapatite platelets in vertebrates. The mineralization of collagen in vitro has gained interest for two reasons: understanding the processes behind bone formation and the synthesis of scaffolds for tissue engineering. In this paper, the efforts toward collagen mineralization in vitro are reviewed. First, general introduction toward collagen type I, the main component of the extracellular matrix in animals, is provided, followed by a brief overview of collagenous skeletons. Then, the in vitro mineralization of collagen is critically reviewed. Due to their biological abundance, hydroxyapatite and silica are the focus of this review. To a much lesser extent, also some efforts with other minerals are outlined. Combining all minerals and the suggested mechanisms for each mineral, a general mechanism for the intrafibrillar mineralization of collagen is proposed. This review concludes with an outlook for further improvement of collagen-based tissue engineering scaffolds.

Replication of a Tissue Microenvironment by Thermal Scanning Probe Lithography

Thermal scanning probe lithography (t-SPL) is a nanofabrication technique in which an immobilized thermolabile resist, such as polyphthalaldehyde (PPA), is locally vaporized by a heated atomic force microscope tip. Compared with other nanofabrication techniques, such as soft lithography and nanoimprinting lithography, t-SPL is more efficient and convenient as it does not involve time-consuming mask productions or complicated etching procedures, making it a promising candidate technique for the fast prototyping of nanoscale topographies for biological studies. Here, we established the direct use of PPA-coated surfaces as a cell culture substrate. We showed that PPA is biocompatible and that the deposition of allylamine by plasma polymerization on a silicon wafer before PPA coating can stabilize the immobilization of PPA in aqueous solutions. When seeded on PPA-coated surfaces, human mesenchymal stem cells (MSC) adhered, spread, and proliferated in a manner indistinguishable from cells cultured on glass surfaces. This allowed us to subsequently use t-SPL to generate nanotopographies for cell culture experiments. As a proof of concept, we analyzed the surface topography of bovine tendon sections, previously shown to induce morphogenesis and differentiation of MSC, by means of atomic force microscopy, and then "wrote" topographical data on PPA by means of t-SPL. The resulting substrate, matching the native tissue topography on the nanoscale, was directly used for MSC culture. The t-SPL substrate induced similar changes in cell morphology and focal adhesion formation in the MSC compared to native tendon sections, suggesting that t-SPL can rapidly generate cell culture substrates with complex and spatially accurate topographical signals. This technique may greatly accelerate the prototyping of models for the study of cell-matrix interactions.

Type-I collagen fibrils: From growth morphology to local order

The length of type-I collagen fibrils in solution increases through the development and progress of pointed tips appearing successively at the two ends of an axis-symmetric shaft with constant diameter. Those tips, respectively fine ([Formula: see text]) or coarse ([Formula: see text]) have opposite molecular orientations. The [Formula: see text]-pointed tips, the first to appear, are particularly remarkable as they all show, on most of their length, a common parabolic profile which stays constant during the growth. Assuming that the latter occurs by lateral accretion of individual molecules in staggered configuration, we propose to give account of this prominent morphological feature along a purely geometrical argument, the profile of a tip being linked to the shape of the trajectories followed all along the accretion process. Among several possible trajectories, Fermat spirals lead to a parabolic profile in perfect agreement with the one observed for [Formula: see text]-pointed tips. This is to be put in relation with the presence of such spirals in phyllotactic patterns which ensure the best packing efficiency in cases of axis-symmetry, which is indeed that of dense collagen fibrils. Moreover, those patterns are structured by concentric circles of dislocations, constitutive of the structure itself, whose behaviour might contribute to the mechanical properties of the fibrils.

A structural prospective for collagen receptors such as DDR and their binding of the collagen fibril

The structure of the collagen fibril surface directly effects and possibly assists the management of collagen receptor interactions. An important class of collagen receptors, the receptor tyrosine kinases of the Discoidin Domain Receptor family (DDR1 and DDR2), are differentially activated by specific collagen types and play important roles in cell adhesion, migration, proliferation, and matrix remodeling. This review discusses their structure and function as it pertains directly to the fibrillar collagen structure with which they interact far more readily than they do with isolated molecular collagen. This prospective provides further insight into the mechanisms of activation and rational cellular control of this important class of receptors while also providing a comparison of DDR-collagen interactions with other receptors such as integrin and GPVI. When improperly regulated, DDR activation can lead to abnormal cellular proliferation activities such as in cancer. Hence how and when the DDRs associate with the major basis of mammalian tissue infrastructure, fibrillar collagen, should be of keen interest.

Synchrotron radiation techniques boost the research in bone tissue engineering

X-ray Synchrotron radiation-based techniques, in particular Micro-tomography and Micro-diffraction, were exploited to investigate the structure of bone deposited in vivo within a porous ceramic scaffold. Bone formation was studied by implanting Mesenchymal Stem Cell (MSC) seeded ceramic scaffolds in a mouse model. Osteoblasts derived from the seeded MSC and from differentiation of cells migrated within the scaffold together with the blood vessels, deposited within the scaffold pores an organic collagenous matrix on which a precursor mineral amorphous liquid-phase, containing Ca++ and PO₄^-- crystallized filling the gaps between the collagen molecules. Histology offered a valid instrument to investigate the engineered tissue structure, but, unfortunately, limited itself to a macroscopic analysis. The evolution of the X-ray Synchrotron radiation-based techniques and the combination of micro X-ray diffraction with X-ray phase-contrast imaging enabled to study the dynamic of the structural and morphological changes occurring during the new bone deposition, biomineralization and vascularization. In fact, the unique features of Synchrotron radiation, is providing the high spatial resolution probe which is necessary for the study of complex materials presenting heterogeneity from micron-scale to meso- and nano-scale. Indeed, this is the occurrence in the heterogeneous and hierarchical bone tissue where an organic matter, such as the collagenous matrix, interacts with mineral nano-crystals to generate a hybrid multiscale biomaterial with unique physical properties. In this framework, the use of advanced synchrotron radiation techniques allowed to understand and to clarify fundamental aspects of the bone formation process within the bioceramic, i.e. biomineralization and vascularization, including to obtain deeper knowledge on bone deposition, mineralization and reabsorption in different health, aging and pathological conditions. In this review we present an overview of the X-ray Synchrotron radiation techniques and we provide a general outlook of their applications on bone Tissue Engineering, with a focus on our group work. STATEMENT OF SIGNIFICANCE: Synchrotron Radiation techniques for Tissue Engineering In this review we report recent applications of X-ray Synchrotron radiation-based techniques, in particular Microtomography and Microdiffraction, to investigations on the structure of ceramic scaffolds and bone tissue regeneration. Tissue engineering has made significant advances in bone regeneration by proposing the use of mesenchymal stem cells in combination with various types of scaffolds. The efficacy of the biomaterials used to date is not considered optimal in terms of resorbability and bone formation, resulting in a poor vascularization at the implant site. The review largely based on our publications in the last ten years could help the study of the regenerative model proposed. We also believe that the new imaging technologies we describe could be a starting point for the development of additional new techniques with the final aim of transferring them to the clinical practice.

Moniliformis cryptosaudi n. sp. (Acanthocephala: Moniliformidae) from the Long-eared Hedgehog Hemiechinus auritus (Gmelin) (Erinaceidae) in Iraq; A Case of Incipient Cryptic Speciation Related to M. saudi in Saudi Arabia

Moniliformis cryptosaudi n. sp. (Moniliformidae) is an acanthocephalan described from the long-eared hedgehog Hemiechinus auritus (Gmelin) (Erinaceidae) in Iraq as an incipient cryptic species of Moniliformis saudi Amin, Heckmann, Mohammed, Evans, 2016 described from the desert hedgehog Paraechinus aethiopicus (Ehrenberg) (Erinaceidae) in Saudi Arabia. Microscopical studies demonstrate that the two species are morphologically indistinguishable with practically identical measurements and counts but differed significantly in their energy dispersive X-ray analysis (EDXA) of metal composition of hooks. Hooks of specimens of the new species appeared to be of collagen material with very low levels of phosphorus and calcium unlike those of M. saudi and Moniliformis kalahariensis Meyer, 1931 that had high levels of calcium and phosphorus. Using 18S rDNA and cox1 genes, M. Saudi and M. kalahariensis were shown to be molecularly distinct but the molecular profiles of M. saudi and M. cryptosaudi were more similar. The molecular profile of M. kalahariensis collected from the South African hedgehog Atelerix frontalis Smith (Erinaceidae) in South Africa is reported for the first time and is studied only for comparative purposes. Moniliformis saudi and M. kalahariensis had comparable EDXA metal analysis that was distinct from that of M. cryptosaudi.

Cryptic binding sites become accessible through surface reconstruction of the type I collagen fibril

Collagen fibril interactions with cells and macromolecules in the extracellular matrix drive numerous cellular functions. Binding motifs for dozens of collagen-binding proteins have been determined on fully exposed collagen triple helical monomers. However, when the monomers are assembled into the functional collagen fibril, many binding motifs become inaccessible, and yet critical cellular processes occur. Here, we have developed an early stage atomic model of the smallest repeating unit of the type I collagen fibril at the fibril surface that provides a novel framework to address questions about these functionally necessary yet seemingly obstructed interactions. We use an integrative approach by combining molecular dynamics (MD) simulations with atomic force microscopy (AFM) experiments and show that reconstruction of the collagen monomers within the complex fibril play a critical role in collagen interactions. In particular, the fibril surface shows three major conformational changes, which allow cryptic binding sites, including an integrin motif involved in platelet aggregation, to be exposed. The observed dynamics and reconstruction of the fibril surface promote its role as a “smart fibril” to keep certain binding sites cryptic, and to allow accessibility of recognition domains when appropriate.

Distributions: The Importance of the Chemist's Molecular View for Biological Materials

Characterization of materials with biological applications and assessment of physiological effects of therapeutic interventions are critical for translating research to the clinic and preventing adverse reactions. Analytical techniques typically used to characterize targeted nanomaterials and tissues rely on bulk measurement. Therefore, the resulting data represent an average structure of the sample, masking stochastic (randomly generated) distributions that are commonly present. In this Perspective, we examine almost 20 years of work our group has done in different fields to characterize and control distributions. We discuss the analytical techniques and statistical methods we use and illustrate how we leverage them in tandem with other bulk techniques. We also discuss the challenges and time investment associated with taking such a detailed view of distributions as well as the risks of not fully appreciating the extent of heterogeneity present in many systems. Through three case studies showcasing our research on conjugated polymers for drug delivery, collagen in bone, and endogenous protein nanoparticles, we discuss how identification and characterization of distributions, i.e., a molecular view of the system, was critical for understanding the observed biological effects. In all three cases, data would have been misinterpreted and insights missed if we had only relied upon spatially averaged data. Finally, we discuss how new techniques are starting to bridge the gap between bulk and molecular level analysis, bringing more opportunity and capacity to the research community to address the challenges of distributions and their roles in biology, chemistry, and the translation of science and engineering to societal challenges.

Structure analysis of collagen fibril at atomic-level resolution and its implications for intra-fibrillar transport in bone biomineralization

Bone is a hierarchical biocomposite material in which a collagen fibril matrix self-assembled in a three-dimensional (3-D) pseudohexagonal array controls many important processes in mineralization such as providing the pathways by which calcium and phosphate species are delivered and a template for the earliest nucleation sites, determining the spatial distribution of the mineral and the topology for binding of associated non-collagenous proteins. However, the structural characteristics of collagen molecules in the fibril remain unclear at the atomic level. Here we performed the first large-scale molecular dynamics simulations to provide a comprehensive all-atom structural analysis of the entire fibril of Type I collagen including intra-fibrillar water distribution. We found that the ideal fibril structure is preserved in specific sites where the earliest nucleation occurs, but is severely distorted in areas that mineralize later. In detail, the ideal pseudohexagonal structure is well-preserved in the overlap zone (c1, c2 and b bands), in the a bands of the hole zone but is severely distorted at the hole/overlap transition (d and c3 bands). As a result, the expected uniform "channel," formed by connecting holes in adjacent unit cells along the b-axis, and having dimensions of 1.5 nm height along the a-axis and width of 40 nm along the c-axis is not formed. The expected uniform channel of 1.5 nm height is preserved only in the a bands in a narrow sub-channel region only 5.8 nm wide. At the hole/overlap transition, an irregular, tortuous sub-channel of widely varying dimensions (∼1.8-4.0 nm height × ∼3.0 nm width) is formed. The well-defined sub-channel in the a bands along with their preferred orientation of charged amino acid residues could facilitate faster molecular diffusion than the tortuous sub-channels and ionic interactions, thus providing the first nucleation sites. Intra-fibrillar water occupies nano-spaces and shows low density (∼0.7 g cm^-3), which should promote dehydration of ion species. These results provide the first atomic-level understanding of the structure of the collagen fibril and the properties of the aqueous compartments within the fibril, which offer a physical, chemical and steric explanation for calcium phosphate infiltration paths and for the initiation of mineralization at the a band collagen fibril. The mechanism revealed here for the observed specificity of collagen biomineralization in bone formation ultimately contributes to the biochemical and biomechanical functions of the skeleton.

Relative orientation of collagen molecules within a fibril: a homology model for homo sapiens type I collagen

Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side chains available at the interface between the molecules.

Revealing Accessibility of Cryptic Protein Binding Sites within the Functional Collagen Fibril

Fibrillar collagens are the most abundant proteins in the extracellular matrix. Not only do they provide structural integrity to all of the connective tissues in the human body, but also their interactions with multiple cell receptors and other matrix molecules are essential to cell functions, such as growth, repair, and cell adhesion. Although specific binding sequences of several receptors have been determined along the collagen monomer, processes by which collagen binding partners recognize their binding sites in the collagen fibril, and the critical driving interactions, are poorly understood. The complex molecular assembly of bundled triple helices within the collagen fibril makes essential ligand binding sites cryptic or hidden from the molecular surface. Yet, critical biological processes that require collagen ligands to have access to interaction sites still occur. In this contribution, we will discuss the molecular packing of the collagen I fibril from the perspective of how collagen ligands access their known binding regions within the fibril, and we will present our analysis of binding site accessibility from the fibril surface. Understanding the basis of these interactions at the atomic level sets the stage for developing drug targets against debilitating collagen diseases and using collagen as drug delivery systems and new biomaterials.

Nanomechanics of Type I Collagen

Type I collagen is the predominant collagen in mature tendons and ligaments, where it gives them their load-bearing mechanical properties. Fibrils of type I collagen are formed by the packing of polypeptide triple helices. Higher-order structures like fibril bundles and fibers are assembled from fibrils in the presence of other collagenous molecules and noncollagenous molecules. Curiously, however, experiments show that fibrils/fibril bundles are less resistant to axial stress compared to their constituent triple helices-the Young's moduli of fibrils/fibril bundles are an order-of-magnitude smaller than the Young's moduli of triple helices. Given the sensitivity of the Young's moduli of triple helices to solvation environment, a plausible explanation is that the packing of triple helices into fibrils perhaps reduces the Young's modulus of an individual triple helix, which results in fibrils having smaller Young's moduli. We find, however, from molecular dynamics and accelerated conformational sampling simulations that the Young's modulus of the buried core of the fibril is of the same order as that of a triple helix in aqueous phase. These simulations, therefore, suggest that the lower Young's moduli of fibrils/fibril bundles cannot be attributed to the specific packing of triple helices in the fibril core. It is not the fibril core that yields initially to axial stress. Rather, it must be the portion of the fibril exposed to the solvent and/or the fibril-fibril interface that bears the initial strain. Overall, this work provides estimates of Young's moduli and persistence lengths at two levels of collagen's structural assembly, which are necessary to quantitatively investigate the response of various biological factors on collagen mechanics, including congenital mutations, posttranslational modifications and ligand binding, and also engineer new collagen-based materials.

Intrafibrillar Mineralization of Self-Assembled Elastin-Like Recombinamer Fibrils

Biomineralization of bone, a controlled process where hydroxyapatite nanocrystals preferentially deposit in collagen fibrils, is achieved by the interplay of the collagen matrix and noncollagenous proteins. Mimicking intrafibrillar mineralization in synthetic systems is highly attractive for the development of advanced hybrid materials with elaborated morphologies and outstanding mechanical properties, as well as understanding the mechanisms of biomineralization. Inspired by nature, intrafibrillar mineralization of collagen fibrils has been successfully replicated in vitro via biomimetic systems, where acidic polymeric additives are used as analogue of noncollagenous proteins in mediating mineralization. The development of synthetic templates that mimic the structure and functions of collagenous matrix in mineralization has yet to be explored. In this study, we demonstrated that self-assembled fibrils of elastin-like recombinamers (ELRs) can induce intrafibrillar mineralization. The ELRs displayed a disordered structure at low temperature but self-assembled into nanofibrils above its inverse transition temperature. In the presence of the self-assembled ELR fibrils, polyaspartate-stabilized amorphous calcium phosphates preferentially infiltrated into the fibrils and then crystallized into hydroxyapatite nanocrystals with their [001] axes aligned parallel to the long axis of the ELR fibril. As the recombinant technology enables designing and producing well-defined ELRs, their molecular and structural properties can be fine-tuned. By examining the ultrastructure of the self-assembled ELRs fibrils as well as their mineralization, we concluded that the spatial confinement formed by a continuum β-spiral structure in an unperturbed fibrillar structure rather than electrostatic interactions or bioactive sequences in the recombinamer composition played the crucial role in inducing intrafibrillar mineralization.

Fibrillar Collagens

Fibrillar collagens (types I, II, III, V, XI, XXIV and XXVII) constitute a sub-group within the collagen family (of which there are 28 types in humans) whose functions are to provide three-dimensional frameworks for tissues and organs. These networks confer mechanical strength as well as signalling and organizing functions through binding to cellular receptors and other components of the extracellular matrix (ECM). Here we describe the structure and assembly of fibrillar collagens, and their procollagen precursors, from the molecular to the tissue level. We show how the structure of the collagen triple-helix is influenced by the amino acid sequence, hydrogen bonding and post-translational modifications, such as prolyl 4-hydroxylation. The numerous steps in the biosynthesis of the fibrillar collagens are reviewed with particular attention to the role of prolyl 3-hydroxylation, collagen chaperones, trimerization of procollagen chains and proteolytic maturation. The multiple steps controlling fibril assembly are then discussed with a focus on the cellular control of this process in vivo. Our current understanding of the molecular packing in collagen fibrils, from different tissues, is then summarized on the basis of data from X-ray diffraction and electron microscopy. These results provide structural insights into how collagen fibrils interact with cell receptors, other fibrillar and non-fibrillar collagens and other ECM components, as well as enzymes involved in cross-linking and degradation.

The supramolecular structure of bone: X-ray scattering analysis and lateral structure modeling

The evolution of vertebrates required a key development in supramolecular evolution: internally mineralized collagen fibrils. In bone, collagen molecules and mineral crystals form a nanocomposite material comparable to cast iron in tensile strength, but several times lighter and more flexible. Current understanding of the internal nanoscale structure of collagen fibrils, derived from studies of rat tail tendon (RTT), does not explain how nucleation and growth of mineral crystals can occur inside a collagen fibril. Experimental obstacles encountered in studying bone have prevented a solution to this problem for several decades. This report presents a lateral packing model for collagen molecules in bone fibrils, based on the unprecedented observation of multiple resolved equatorial reflections for bone tissue using synchrotron small-angle X-ray scattering (SAXS; ∼1 nm resolution). The deduced structure for pre-mineralized bone fibrils includes features that are not present in RTT: spatially discrete microfibrils. The data are consistent with bone microfibrils similar to pentagonal Smith microfibrils, but are not consistent with the (nondiscrete) quasi-hexagonal microfibrils reported for RTT. These results indicate that collagen fibrils in bone and tendon differ in their internal structure in a manner that allows bone fibrils, but not tendon fibrils, to internally mineralize. In addition, the unique pattern of collagen cross-link types and quantities in mineralized tissues can be can be accounted for, in structural/functional terms, based on a discrete microfibril model.

Enigmatic insight into collagen

Collagen is a unique, triple helical molecule which forms the major part of extracellular matrix. It is the most abundant protein in the human body, representing 30% of its dry weight. It is the fibrous structural protein that makes up the white fibers (collagen fibers) of skin, tendons, bones, cartilage and all other connective tissues. Collagens are not only essential for the mechanical resistance and resilience of multicellular organisms, but are also signaling molecules defining cellular shape and behavior. The human body has at least 16 types of collagen, but the most prominent types are I, II and III. Collagens are produced by several cell types and are distinguishable by their molecular compositions, morphologic characteristics, distribution, functions and pathogenesis. This is the major fibrous glycoprotein present in the extracellular matrix and in connective tissue and helps in maintaining the structural integrity of these tissues. It has a triple helical structure. Various studies have proved that mutations that modify folding of the triple helix result in identifiable genetic disorders. Collagen diseases share certain similarities with autoimmune diseases, because autoantibodies specific to each collagen disease are produced. Therefore, this review highlights the role of collagen in normal health and also the disorders associated with structural and functional defects in collagen.

Investigation of ethanol infiltration into demineralized dentin collagen fibrils using molecular dynamics simulations

The purpose of this study is to investigate the interaction of neat ethanol with bound and non-bound water in completely demineralized dentin that is fully hydrated, using molecular dynamics (MD) simulation method. The key to creating ideal resin-dentin bonds is the removal of residual free water layers and its replacement by ethanol solvent in which resin monomers are soluble, using the ethanol wet-bonding technique. The test null hypotheses were that ethanol cannot remove any collagen-bound water, and that ethanol cannot infiltrate into the spacing between collagen triple helix due to narrow interlayer spacing. Collagen fibrillar structures of overlap and gap regions were constructed by aligning the collagen triple helix of infinite length in hexagonal packing. Three layers of the water molecules were specified as the layers of 0.15-0.22nm, 0.22-0.43nm and 0.43-0.63nm from collagen atoms by investigating the water distribution surrounding collagen molecules. Our simulation results show that ethanol molecules infiltrated into the intermolecular spacing in the gap region, which increased due to the lateral shrinkage of the collagen structures in contact with ethanol solution, while there was no ethanol infiltration observed in the overlap region. Infiltrated ethanol molecules in the gap region removed residual water molecules via modifying mostly the third water layer (50% decrease), which would be considered as a loosely-bound water layer. The first and second hydration layers, which would be considered as tightly bound water layers, were not removed by the ethanol molecules, thus maintaining the helical structures of the collagen molecules.

Articular cartilage: from formation to tissue engineering

Hyaline cartilage is the nonlinear, inhomogeneous, anisotropic, poro-viscoelastic connective tissue that serves as friction-reducing and load-bearing cushion in synovial joints and is vital for mammalian skeletal movements. Due to its avascular nature, low cell density, low proliferative activity and the tendency of chondrocytes to de-differentiate, cartilage cannot regenerate after injury, wear and tear, or degeneration through common diseases such as osteoarthritis. Therefore severe damage usually requires surgical intervention. Current clinical strategies to generate new tissue include debridement, microfracture, autologous chondrocyte transplantation, and mosaicplasty. While articular cartilage was predicted to be one of the first tissues to be successfully engineered, it proved to be challenging to reproduce the complex architecture and biomechanical properties of the native tissue. Despite significant research efforts, only a limited number of studies have evolved up to the clinical trial stage. This review article summarizes the current state of cartilage tissue engineering in the context of relevant biological aspects, such as the formation and growth of hyaline cartilage, its composition, structure and biomechanical properties. Special attention is given to materials development, scaffold designs, fabrication methods, and template-cell interactions, which are of great importance to the structure and functionality of the engineered tissue.

Thermal Destabilization of Collagen Matrix Hierarchical Structure by Freeze/Thaw

This study aims to characterize and understand the effects of freezing on collagen structures and functionality. Specifically, thermodynamic destabilization of collagen at molecular- and fibril-levels by combination of low temperatures and freezing were experimentally characterized using modulated differential scanning calorimetry. In order to delineate the effects of sub-zero temperature and water-ice phase change, we hypothesized that the extent of destabilization can be determined based on post-thaw heat induced thermal denaturation of collagen. It is found that thermal denaturation temperature of collagen in hydrogel decreases by 1.4–1.6°C after freeze/thaw while no such decrease is observed in the case of molecular solution. The destabilization is predominantly due to ice formation. Exposure to low temperatures in the absence of ice has only minimal effect. Calorimetry measurements combined with morphological examination of collagen matrices by scanning electron microscopy suggest that freezing results in destabilization of collagen fibrils due to expansion of intrafibrillar space by ice formation. This fibril-level damage can be alleviated by use of cryoprotectant DMSO at concentrations as low as 0.5 M. A theoretical model explaining the change in collagen post-thaw thermal stability by freezing-induced fibril expansion is also proposed.

A perspective on structural and computational work on collagen

Collagen is the single most abundant protein in the extracellular matrix in the animal kingdom, with remarkable structural and functional diversity and regarded one of the most useful biomaterials.

Imaging collagen packing dynamics during mineralization of engineered bone tissue

The structure and organization of the Type I collagen microfibrils during mineral nanoparticle formation appear as the key factor for a deeper understanding of the biomineralization mechanism and for governing the bone tissue physical properties. In this work we investigated the dynamics of collagen packing during ex-vivo mineralization of ceramic porous hydroxyapatite implant scaffolds using synchrotron high resolution X-ray phase contrast micro-tomography (XPCμT) and synchrotron scanning micro X-ray diffraction (SμXRD). While XPCμT provides the direct 3D image of the collagen fibers network organization with micrometer spatial resolution, SμXRD allows to probe the structural statistical fluctuations of the collagen fibrils at nanoscale. In particular we imaged the lateral spacing and orientation of collagen fibrils during the anisotropic growth of mineral nanocrystals. Beyond throwing light on the bone regeneration multiscale process, this approach can provide important information in the characterization of tissue in health, aging and degeneration conditions.

STATEMENT OF SIGNIFICANCE

BONE grafts are the most common transplants after the blood transfusions. This makes the bone-tissue regeneration research of pressing scientific and social impact. Bone is a complex hierarchical structure, where the interplay of organic and inorganic mineral phases at different length scale (from micron to atomic scale) affect its functionality and health. Thus, the understanding of bone tissue regeneration requires to image its spatial-temporal evolution (i) with high spatial resolution and (ii) at different length scale. We exploited high spatial resolution X-ray Phase Contrast micro Tomography and Scanning micro X-ray Diffraction in order to get new insight on the engineered tissue formation mechanisms. This approach could open novel routes for the early detection of different degenerative conditions of tissue.

Effect of intrinsic and extrinsic factors on the simulated D-band length of type I collagen

A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple-helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers. This organization is visible distinctly in the microfibrillar model of collagen obtained from fiber diffraction. However, to date, no atomistic simulations of this diffraction model under zero-stress conditions have reported a preservation of this structural feature. Such a demonstration is important as it provides the baseline to infer response functions of physiological stimuli. In contrast, simulations predict a considerable shrinkage of the D-band (11-19%). Here we evaluate systemically the effect of several factors on D-band shrinkage. Using force fields employed in previous studies we find that irrespective of the temperature/pressure coupling algorithms, assumed salt concentration or hydration level, and whether or not the monomers are cross-linked, the D-band shrinks considerably. This shrinkage is associated with the bending and widening of individual monomers, but employing a force field whose backbone dihedral energy landscape matches more closely with our computed CCSD(T) values produces a small D-band shrinkage of < 3%. Since this force field also performs better against other experimental data, it appears that the large shrinkage observed in earlier simulations is a force-field artifact. The residual shrinkage could be due to the absence of certain atomic-level details, such as glycosylation sites, for which we do not yet have suitable data.

Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens

Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ∼ 67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.

From nano to macro: studying the hierarchical structure of the corneal extracellular matrix

In this review, we discuss current methods for studying ocular extracellular matrix (ECM) assembly from the 'nano' to the 'macro' levels of hierarchical organization. Since collagen is the major structural protein in the eye, providing mechanical strength and controlling ocular shape, the methods presented focus on understanding the molecular assembly of collagen at the nanometre level using X-ray scattering through to the millimetre to centimetre level using non-linear optical (NLO) imaging of second harmonic generated (SHG) signals. Three-dimensional analysis of ECM structure is also discussed, including electron tomography, serial block face scanning electron microscopy (SBF-SEM) and digital image reconstruction. Techniques to detect non-collagenous structural components of the ECM are also presented, and these include immunoelectron microscopy and staining with cationic dyes. Together, these various approaches are providing new insights into the structural blueprint of the ocular ECM, and in particular that of the cornea, which impacts upon our current understanding of the control of corneal shape, pathogenic mechanisms underlying ectatic disorders of the cornea and the potential for corneal tissue engineering.

Influence of Crosslink Density and Stiffness on Mechanical Properties of Type I Collagen Gel

The mechanical properties of type I collagen gel vary due to different polymerization parameters. In this work, the role of crosslinks in terms of density and stiffness on the macroscopic behavior of collagen gel were investigated through computational modeling. The collagen fiber network was developed in a representative volume element, which used the inter-fiber spacing to regulate the crosslink density. The obtained tensile behavior of collagen gel was validated against published experimental data. Results suggest that the cross-linked fiber alignment dominated the strain stiffening effect of the collagen gel. In addition, the gel stiffness was enhanced approximately 40 times as the crosslink density doubled. The non-affine deformation was reduced with the increased crosslink density. A positive bilinear correlation between the crosslink density and gel stiffness was obtained. On the other hand, the crosslink stiffness had much less impact on the gel stiffness. This work could enhance our understanding of collagen gel mechanics and shed lights on designing future clinical relevant biomaterials with better control of polymerization parameters.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues

The critical role of the self-assembled structure of collagen in skeletal mineralization is long recognized, yet the angstrom to tens of nanometers length-scale nucleation mechanism of calcium phosphate mineral (Ca-Pi) remains unclear. Here, by constructing three-dimensional structure of collagen fibril, we report direct computational evidence of intrafibrillar Ca-Pi nucleation in the collagen matrix and illustrate the crucial role of charged amino acid sidechains of collagen molecules in nucleation. The all-atom Hamiltonian replica exchange molecular dynamics simulation shows that these charged sidechains are oriented toward the fibril "hole zones" and significantly template nucleation with amorphous Ca-Pi phase, ∼1.3-1.6 nm in size, thus explaining the empirical observations that Ca-Pi nucleates principally in these regions. We also show that the low water density of about 0.70 g cm(-3) in these zones may further benefit nucleation by lowering the enthalpic penalty for ion desolvation. This work provides insight, at the atomistic level, into the nucleation mechanism of bone crystals within a collagen matrix for understanding mineral deposition, interpreting mineralization experiments and guiding the design of new implantable materials.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Extracellular matrix assembly: a multiscale deconstruction

The biochemical and biophysical properties of the extracellular matrix (ECM) dictate tissue-specific cell behaviour. The molecules that are associated with the ECM of each tissue, including collagens, proteoglycans, laminins and fibronectin, and the manner in which they are assembled determine the structure and the organization of the resultant ECM. The product is a specific ECM signature that is comprised of unique compositional and topographical features that both reflect and facilitate the functional requirements of the tissue.

Self-assembly of fiber-forming collagen mimetic peptides controlled by triple-helical nucleation

Mimicking the multistep self-assembly of the fibrillar protein collagen is an important design challenge in biomimetic supramolecular chemistry. Utilizing the complementarity of oppositely charged domains in short collagen-like peptides, we have devised a strategy for the self-assembly of these peptides into fibers. The strategy depends on the formation of a staggered triple helical species facilitated by interchain charged pairs, and is inspired by similar sticky-ended fibrillation designs applied in DNA and coiled coil fibers. We compare two classes of collagen mimetic peptides with the same composition but different domain arrangements, and show that differences in their proposed nucleation events differentiates their fibrillation capabilities. Larger nucleation domains result in rapid fiber formation and eventual precipitation or gelation while short nucleation domains leave the peptide soluble for long periods of time. For one of the fiber-forming peptides, we elucidate the packing parameters by X-ray diffraction.

Increasing Thermal Stability of Gelatin by UV-Induced Cross-Linking with Glucose

The effects of ultraviolet (254 nm) radiation on a hydrated gelatin-glucose matrix were investigated for the development of a physiologically thermostable substrate for potential use in cell scaffold production. Experiments conducted with a differential scanning calorimeter indicate that ultraviolet irradiation of gelatin-glucose hydrogels dramatically increases thermal stability such that no melting is observed at temperatures of at least 90°C. The addition of glucose significantly increases the yield of cross-linked product, suggesting that glucose has a role in cross-link formation. Comparisons of lyophilized samples using scanning electron microscopy show that irradiated materials have visibly different densities.

Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen

Clostridial collagenases are among the most efficient degraders of collagen. Most clostridia are saprophytes and secrete proteases to utilize proteins in their environment as carbon sources; during anaerobic infections, collagenases play a crucial role in host colonization. Several medical and biotechnological applications have emerged utilizing their high collagenolytic efficiency. However, the contribution of the functionally most important peptidase domain to substrate specificity remains unresolved. We investigated the active site sequence specificity of the peptidase domains of collagenase G and H from Clostridium histolyticum and collagenase T from Clostridium tetani. Both prime and non-prime cleavage site specificity were simultaneously profiled using Proteomic Identification of protease Cleavage Sites (PICS), a mass spectrometry-based method utilizing database searchable proteome-derived peptide libraries. For each enzyme we identified > 100 unique-cleaved peptides, resulting in robust cleavage logos revealing collagen-like specificity patterns: a strong preference for glycine in P3 and P1′, proline at P2 and P2′, and a slightly looser specificity at P1, which in collagen is typically occupied by hydroxyproline. This specificity for the classic collagen motifs Gly-Pro-X and Gly-X-Hyp represents a remarkable adaptation considering the complex requirements for substrate unfolding and presentation that need to be fulfilled before a single collagen strand becomes accessible for cleavage.

Biological significance

We demonstrate the striking sequence specificity of a family of clostridial collagenases using proteome derived peptide libraries and PICS, Proteomic Identification of protease Cleavage Sites. In combination with the previously published crystal structures of these proteases, our results represent an important piece of the puzzle in understanding the complex mechanism underlying collagen hydrolysis, and pave the way for the rational design of specific test substrates and selective inhibitors.

This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?

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Active site specificity profiling of 3 clostridial collagenases—ColG and H from C. histolyticum, and ColT from C. tetani.

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Their high sequence specificity to collagen-like sequence points towards a co-evolution with the mammalian substrate.

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Significant differences to MMPs and a more promiscuous cleavage mechanism facilitating rapid collagenolysis were revealed.

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Human proteome-derived peptide libraries & PICS are suitable for active site specificity profiling of pathogenic proteases.

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Results pave the way for rational design of test substrates and selective inhibitors.

Piezoelectric properties of aligned collagen membranes

Electromechanical coupling, a phenomenon present in collagenous materials, may influence cell-extracellular matrix interactions. Here, electromechanical coupling has been investigated via piezoresponse force microscopy in transparent and opaque membranes consisting of helical-like arrays of aligned type I collagen fibrils self-assembled from acidic solution. Using atomic force microscopy, the transparent membrane was determined to contain fibrils having an average diameter of 76 ± 14 nm, whereas the opaque membrane comprised fibrils with an average diameter of 391 ± 99 nm. As the acidity of the membranes must be neutralized before they can serve as cell culture substrates, the structure and piezoelectric properties of the membranes were measured under ambient conditions before and after the neutralization process. A crimp structure (1.59 ± 0.37 µm in width) perpendicular to the fibril alignment became apparent in the transparent membrane when the pH was adjusted from acidic (pH = 2.5) to neutral (pH = 7) conditions. In addition, a 1.35-fold increase was observed in the amplitude of the shear piezoelectricity of the transparent membrane. The structure and piezoelectric properties of the opaque membrane were not significantly affected by the neutralization process. The results highlight the presence of an additional translational order in the transparent membrane in the direction perpendicular to the fibril alignment. The piezoelectric response of both membrane types was found to be an order of magnitude lower than that of collagen fibrils in rat tail tendon. This reduced response is attributed to less-ordered molecular assembly than is present in D-periodic collagen fibrils, as evidenced by the absence of D-periodicity in the membranes.

Collagen--emerging collagen based therapies hit the patient

The choice of biomaterials available for regenerative medicine continues to grow rapidly, with new materials often claiming advantages over the short-comings of those already in existence. Going back to nature, collagen is one of the most abundant proteins in mammals and its role is essential to our way of life. It can therefore be obtained from many sources including porcine, bovine, equine or human and offer a great promise as a biomimetic scaffold for regenerative medicine. Using naturally derived collagen, extracellular matrices (ECMs), as surgical materials have become established practice for a number of years. For clinical use the goal has been to preserve as much of the composition and structure of the ECM as possible without adverse effects to the recipient. This review will therefore cover in-depth both naturally and synthetically produced collagen matrices. Furthermore the production of more sophisticated three dimensional collagen scaffolds that provide cues at nano-, micro- and meso-scale for molecules, cells, proteins and bulk fluids by inducing fibrils alignments, embossing and layered configuration through the application of plastic compression technology will be discussed in details. This review will also shed light on both naturally and synthetically derived collagen products that have been available in the market for several purposes including neural repair, as cosmetic for the treatment of dermatologic defects, haemostatic agents, mucosal wound dressing and guided bone regeneration membrane. There are other several potential applications of collagen still under investigations and they are also covered in this review.

Type I collagen self-assembly: the roles of substrate and concentration

Collagen molecules, self-assembled into macroscopic hierarchical tissue networks, are the main organic building block of many biological tissues. A particularly common and important form of this self-assembly consists of type I collagen fibrils, which exhibit a nanoscopic signature, D-periodic gap/overlap spacing, with a distribution of values centered at approximately 67 nm. In order to better understand the relationship between type I collagen self-assembly and D-spacing distribution, we investigated surface-mediated collagen self-assembly as a function of substrate and incubation concentration. Collagen fibril assembly on phlogopite and muscovite mica as well as fibrillar gel coextrusion in glass capillary tubes all exhibited D-spacing distributions similar to those commonly observed in biological tissues. The observation of D-spacing distribution by self-assembly of type I collagen alone is significant as it eliminates the necessity to invoke other preassembly or postassembly hypotheses, such as variation in the content of collagen types, enzymatic cross-linking, or other post-translational modifications, as mechanistic origins of D-spacing distribution. The D-spacing distribution on phlogopite mica is independent of type I collagen concentration, but on muscovite mica D-spacing distributions showed increased negative skewness at 20 μg/mL and higher concentrations. Tilted D-spacing angles were found to correlate with decreased D-spacing measurements, an effect that can be removed with a tilt angle correction, resulting in no concentration dependence of D-spacing distribution on muscovite mica. We then demonstrated that tilted D-spacing is uncommon in biological tissues and it does not explain previous observations of low D-spacing values in ovariectomized dermis and bone.