The in situ supermolecular structure of type I collagen

Effects of probe pollutants on morphological and mechanical measurements of muscle and collagen fibers using atomic force microscopy

Because of the interaction between probes and samples, pollutants in buffer solution or in the air would easily bind to probes and make the probe polluted, which might influence the morphological and mechanical measurements with atomic force microscopy. The polluted probes might transfer the pollutants onto the samples and thus change the surface ultrastructure of samples, or collect the deviated feedback signals to make the phantasm images. The former process is irreversible even if a new probe is employed, and the latter one is a reversible process as long as changing the used/polluted probe. Effects of polluted probes on morphological and mechanical characteristics of insect flight muscle and rat tail tendon collagen I fibers had been discussed in this study, in which, we constructed a series of methods to avoid/reduce the collecting of phantasm images and deviated mechanical information, such as changing the scanning direction and scanning force, replacing the new probes, or cleaning the polluted probes.

Nanoscale measurements of the assembly of collagen to fibrils

Observing the self-assembly of collagen from single collagen monomers to higher order fibrils and fibers provides a bottom-up approach to engineering its ultrastructure in comparison to structural studies of already formed collagen fibers. This approach can be used for the fabrication of controlled collagen-based biomaterials with varying mechanical properties. Here, we investigate the time-dependent self-assembly of collagen into single fibrils in vitro through high resolution imaging of collagen type 1 prior to fibrillogenesis. This was confirmed by comparing persistence length and diameter in controlled experiments and studying the morphology and mechanical properties of nanoscale collagen fibrils through AFM nanoindentation measurements. The Young's modulus of these collagen fibrils was estimated to be around 1GPa in the dehydrated state. The stability and mechanical characteristics of collagen obtained in these experiments indicate the hierarchical assembly occurs at both a structural and mechanical level.

Visualization of the nanoscale assembly of type I collagen on PLA by AFM

Collagen adsorption and the morphology of its assemblies at polymer surface play an important role in improving the biocompatibility of materials. In this study, the nanoscale organization of type I collagen on Polylactide (PLA) was observed directly by high-resolution atomic force microscopy. The results show that the supramolecular structure of adsorbed collagen was affected by the concentration of collagen solution, appropriate pH and electrolyte composition of the buffer. On PLA substrate, network structures formed in high humidity atmosphere. In addition, collagen formed well-oriented nano-patterns at nearly neutral pH and appropriate electrolyte composition. Particularly, the typical 65 nm D-periodicity of collagen fibers was observed in the presence of potassium ions. Our investigation provides useful insights into the regulation of collagen assembly by substrates and environmental conditions, which is important for understanding the mechanism of collagen adsorption and assembly on polymer surfaces. It also offers a potential way to create surfaces of bio-functioned and nano-patterned materials for biotechnological and biomedical applications.

Conformational selection and collagenolysis in type III collagen

Matrix metalloproteases (MMPs) cleave native collagen at a single site despite the fact that collagen contains more than one scissile bond that can, in principle, be cleaved. For peptide bond hydrolysis to occur at one specific site, MMPs must (1) localize to a region near the unique scissile bond, (2) bind residues at the catalytic site that form the scissile bond, and (3) hydrolyze the corresponding peptide bond. Prior studies suggest that for some types of collagen, binding of noncatalytic MMP domains to amino acid sequences in the vicinity of the true cleavage site facilitates the localization of collagenases. In the present study, our goal was to determine whether binding to the catalytic site also plays a role in determining MMP specificity. To investigate this, we computed the conformational free energy landscape of Type III collagen at each potential cleavage site. The free energy profiles suggest that although all potential cleavage sites sample unfolded states at relatively low temperatures, the true cleavage site samples structures that are complementary to the catalytic site. By contrast, potential cleavage sites that are not cleaved sample states that are relatively incompatible with the MMP active site. Furthermore, our findings point to a specific role for arginine residues in modulating the structural stability of collagen near the collagenase cleavage site. These data imply that locally unfolded potential cleavage sites in Type III collagen sample distinct unfolded ensembles, and that the region about the true collagenase cleavage site samples states that are most complementary to the MMP active site.

In situ D-periodic molecular structure of type II collagen

Collagens are essential components of extracellular matrices in multicellular animals. Fibrillar type II collagen is the most prominent component of articular cartilage and other cartilage-like tissues such as notochord. Its in situ macromolecular and packing structures have not been fully characterized, but an understanding of these attributes may help reveal mechanisms of tissue assembly and degradation (as in osteo- and rheumatoid arthritis). In some tissues such as lamprey notochord, the collagen fibrillar organization is naturally crystalline and may be studied by x-ray diffraction. We used diffraction data from native and derivative notochord tissue samples to solve the axial, D-periodic structure of type II collagen via multiple isomorphous replacement. The electron density maps and heavy atom data revealed the conformation of the nonhelical telopeptides and the overall D-periodic structure of collagen type II in native tissues, data that were further supported by structure prediction and transmission electron microscopy. These results help to explain the observed differences in collagen type I and type II fibrillar architecture and indicate the collagen type II cross-link organization, which is crucial for fibrillogenesis. Transmission electron microscopy data show the close relationship between lamprey and mammalian collagen fibrils, even though the respective larger scale tissue architecture differs.

Nanomechanical heterogeneity in the gap and overlap regions of type I collagen fibrils with implications for bone heterogeneity

The microstructure of type I collagen, consisting of alternating gap and overlap regions with a characteristic D period of approximately 67 nm, enables multifunctionalities of collagen fibrils in different tissues. Implementing near-surface dynamic and static nanoindentation techniques with atomic force microscope, we reveal mechanical heterogeneity along the axial direction of a single isolated collagen fibril from tendon and show that, within the D period, the gap and overlap regions have significantly different elastic and energy dissipation properties, correlating the significantly different molecular structures in these two regions. We further show that such subfibrillar heterogeneity holds in collagen fibrils inside bone and might be intrinsically related to the excellent energy dissipation performance of bone.

Molecular and mesoscale mechanisms of osteogenesis imperfecta disease in collagen fibrils

Osteogenesis imperfecta (OI) is a genetic disorder in collagen characterized by mechanically weakened tendon, fragile bones, skeletal deformities, and in severe cases, prenatal death. Although many studies have attempted to associate specific mutation types with phenotypic severity, the molecular and mesoscale mechanisms by which a single point mutation influences the mechanical behavior of tissues at multiple length scales remain unknown. We show by a hierarchy of full atomistic and mesoscale simulation that OI mutations severely compromise the mechanical properties of collagenous tissues at multiple scales, from single molecules to collagen fibrils. Mutations that lead to the most severe OI phenotype correlate with the strongest effects, leading to weakened intermolecular adhesion, increased intermolecular spacing, reduced stiffness, as well as a reduced failure strength of collagen fibrils. We find that these molecular-level changes lead to an alteration of the stress distribution in mutated collagen fibrils, causing the formation of stress concentrations that induce material failure via intermolecular slip. We believe that our findings provide insight into the microscopic mechanisms of this disease and lead to explanations of characteristic OI tissue features such as reduced mechanical strength and a lower cross-link density. Our study explains how single point mutations can control the breakdown of tissue at much larger length scales, a question of great relevance for a broad class of genetic diseases.

Effects of Cr3+ on the structure of collagen fiber

We have investigated the effects of Cr3+ on the hierarchical structure of pigskin collagen fibers by use of scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), wide-angle X-ray diffraction (WAXD), confocal laser micro-Raman spectroscopy (CLRS), and circular dichroism (CD). Our results demonstrate that the introduction of Cr3+ leads to the formation of a cluster of 20-40 nm between collagen fibrils, while the unique axial periodic structure (D periodicity) of the fibrils does not change. As the Cr3+ concentration increases, the order of intermolecular lateral packing, crystallite structure within helical chains, and N and C telopeptide regions decrease. The present study reveals that Cr3+ only cross-links with collagen but does not disrupt its triple helical structure.

Structural insights into the interactions between platelet receptors and fibrillar collagen

Collagen peptides have been used to identify binding sites for several important collagen receptors, including integrin alpha(2)beta(1), glycoprotein VI, and von Willebrand factor. In parallel, the structures of these collagen receptors have been reported, and their interactions with collagen peptides have been studied. Recently, the three-dimensional structure of the intact type I collagen fiber from rat tail tendon has been resolved by fiber diffraction. It is now possible to map the binding sites of platelet collagen receptors onto the intact collagen fiber in three dimensions. This minireview will discuss these recent findings and their implications for platelet activation by collagen.

Fiber diffraction of skin and nails provides an accurate diagnosis of malignancies

An early diagnosis of malignancies correlates directly with a better prognosis. Yet for many malignancies there are no readily available, noninvasive, cost-effective diagnostic tests with patients often presenting too late for effective treatment. This article describes for the first time the use of fiber diffraction patterns of skin or fingernails, using X-ray sources, as a biometric diagnostic method for detecting neoplastic disorders including but not limited to melanoma, breast, colon and prostate cancers. With suitable further development, an early low-cost, totally noninvasive yet reliable diagnostic test could be conducted on a regular basis in local radiology facilities, as a confirmatory test for other diagnostic procedures or as a mass screening test using suitable small angle X-ray beam-lines at synchrotrons.

Collagen structure and stability

Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen-the prototypical collagen fibril-has been revealed in detail. Artificial collagen fibrils that display some properties of natural collagen fibrils are now accessible using chemical synthesis and self-assembly. A rapidly emerging understanding of the mechanical and structural properties of native collagen fibrils will guide further development of artificial collagenous materials for biomedicine and nanotechnology.

Self-assembly nano-structure of type I collagen adsorbed on Gemini surfactant LB monolayers

The self-assembly nano-structures of type I collagen adsorbed on anionic Gemini surfactant LB monolayer were observed by using atomic force microscopy (AFM) images. It was found that the adsorption behavior and self-assembly structure of collagen could be controlled by the concentration of the collagen solution, adsorption interval and the properties of substrates. With the increase of the adsorption interval and concentration of collagen, the strands size of collagen changed. The self-assembly structures of collagen were also influenced by the interaction between collagen molecules and Gemini surfactant monolayer substrates. Finally, the adsorption behaviors of collagen molecules on cationic Gemini monolayer were compared with those on anionic Gemini monolayer.

A finite dissipative theory of temporary interfibrillar bridges in the extracellular matrix of ligaments and tendons

The structural integrity and the biomechanical characteristics of ligaments and tendons result from the interactions between collagenous and non-collagenous proteins (e.g. proteoglycans, PGs) in the extracellular matrix. In this paper, a dissipative theory of temporary interfibrillar bridges in the anisotropic network of collagen type I, embedded in a ground substance, is derived. The glycosaminoglycan chains of decorin are assumed to mediate interactions between fibrils, behaving as viscous structures that transmit deformations outside the collagen molecules. This approach takes into account the dissipative effects of the unfolding preceding fibrillar elongation, together with the slippage of entire fibrils and the strain-rate-dependent damage evolution of the interfibrillar bridges. Thermodynamic consistency is used to derive the constitutive equations, and the transition state theory is applied to model the rearranging properties of the interfibrillar bridges. The constitutive theory is applied to reproduce the hysteretic spectrum of the tissues, demonstrating how PGs determine damage evolution, softening and non-recoverable strains in their cyclic mechanical response. The theoretical predictions are compared with the experimental response of ligaments and tendons from referenced studies. The relevance of the proposed model in mechanobiology research is discussed, together with several applications from medical practice to bioengineering science.

Mineral deposition in the extracellular matrices of vertebrate tissues: identification of possible apatite nucleation sites on type I collagen

The possible means by which type I collagen may mediate mineralization in normal vertebrate bone, tendon, dentin and cementum as well as in pathological mineral formation are not fully understood. One consideration in this regard is that the structure of the protein is somehow important in binding calcium and phosphate ions in a stereochemical configuration conducive to nucleation of apatite crystals. In the present study, type I collagen, packed in a quarter-staggered arrangement in two dimensions and a quasi-hexagonal model of microfibrillar assembly in three dimensions, has been examined in terms of several of its charged amino acid residues. These included glutamic and aspartic acid, lysine, arginine, hydroxylysine and histidine, whose positions along the three alpha-chain axes of the collagen molecule were determined with respect to each other. It was found that the locations of these residues specified sites uniquely suited as potential apatite nucleation centers following binding of calcium and phosphate ions. From this analysis, it would appear that type I collagen provides a template of charged amino acid residues that dictates ion binding critical to subsequent nucleation events for mineral formation in vertebrate tissues.

Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis

We describe the molecular structure of the collagen fibril and how it affects collagen proteolysis or "collagenolysis." The fibril-forming collagens are major components of all mammalian connective tissues, providing the structural and organizational framework for skin, blood vessels, bone, tendon, and other tissues. The triple helix of the collagen molecule is resistant to most proteinases, and the matrix metalloproteinases that do proteolyze collagen are affected by the architecture of collagen fibrils, which are notably more resistant to collagenolysis than lone collagen monomers. Until now, there has been no molecular explanation for this. Full or limited proteolysis of the collagen fibril is known to be a key process in normal growth, development, repair, and cell differentiation, and in cancerous tumor progression and heart disease. Peptide fragments generated by collagenolysis, and the conformation of exposed sites on the fibril as a result of limited proteolysis, regulate these processes and that of cellular attachment, but it is not known how or why. Using computational and molecular visualization methods, we found that the arrangement of collagen monomers in the fibril (its architecture) protects areas vulnerable to collagenolysis and strictly governs the process. This in turn affects the accessibility of a cell interaction site located near the cleavage region. Our observations suggest that the C-terminal telopeptide must be proteolyzed before collagenase can gain access to the cleavage site. Collagenase then binds to the substrate's "interaction domain," which facilitates the triple-helix unwinding/dissociation function of the enzyme before collagenolysis.

A structural informatics study on collagen

The study integrates knowledge resulting from structure-activity relationships analysis of amino acids with respect to the characterization of alpha1 and alpha2 type I collagen chains. Specifically, 15 amino acids and 14 properties were investigated and their structure-activity relationship models were obtained. The models were integrated into a web application and were used to predict the properties of a set of six amino acids. The similarities in alpha1 and alpha2 type I collagen chains has been investigated starting from the observed and predicted properties of amino acids by using two-step cluster analysis.

An in situ study of collagen self-assembly processes

We present in situ studies on the self-assembly and dynamic evolution of collagen gels from semidilute solutions in a microfluidic device. Collagen fibrils not only reinforce the mechanical properties of bone and tissues, but they also influence cellular motility and morphology. We access the initial steps of the hierarchical self-assembly of collagen fibrils and networks by using hydrodynamic focusing to form oriented fibers. The accurate description of the conditions within the microchannel requires a numerical expression for the pH in the device as well as a modified mathematical description of the viscosity, which increases nearly 300-fold as collagen fibrils form around neutral pH. Finite element modeling profiles overlay impressively with cross-polarized microscopy images of the birefringent fibrils in the channel. Real-time X-ray microdiffraction measurements in flow indicate an enhanced supramolecular packing having a unit spacing commensurate with that of a pentameric collagen subunit. These results have significant implications for the field of biomedicine, wherein new aligned, cellularly active, and mechanically strengthened materials continue to be in demand. However, this work is also remarkable from a more fundamental, biophysical point of view because the underlying concepts may be generalized to a large pool of systems.

Nano finite element modeling of the mechanical behavior of biocomposites using multi-scale (virtual internal bond) material models

It is evident that biocomposites, specifically mineralized Type-I collagen fibrils, have strong mechanical properties, such as a desirable combination of elastic modulus, fracture toughness, and fracture strength. The mineral Hydroxyapatite [Hap] by itself is stiffer, and it is not clear whether a collagen fiber by itself has a lower breaking strength than the mineralized fiber. Hence, the objective of this paper is to develop, outline, apply, and demonstrate issues involving a new nano explicit finite element based framework, by which the mechanical behavior of mineralized collagen fibrils and their constituents can be studied. A multi-scale virtual internal bond model is used to model the material behavior and failure of such biocomposites. In this research two models have been studied. The first model attempts to illustrate the hypothesis that materials are less sensitive to flaws at nanoscale and the second model studies the mechanical behavior of a nano sized dahlite mineral crystal commonly found in collagen fibril. Two important implementation characteristics have been introduced and illustrated, namely that scaled properties can be used at the micro and nano length scales along with scaled dimensions and secondly the loading time can be appropriately scaled without the loading becoming a dynamic loading.

Biochemistry and functional significance of collagen cross-linking

The biophysical characteristics of vascular tissues are dependent largely on the properties of fibrillar collagens. Considering the predominant structural component, collagen type I, the present review describes the mechanisms of formation and maturation of lysyl oxidase-mediated cross-linking, leading to an understanding of how intracellular collagen-modifying enzymes affect the patterns of cross-links produced. An important distinction is made between the enzyme-mediated cross-linking, essential for optimum tissue function, and the non-enzymatic aging processes that generally lead to structural changes deleterious to function. Finally, the extracellular matrix of vascular tissue is a multicomponent system and the role of other major constituents, such as elastin and glycosaminoglycans, in modifying tissue properties should be considered. Some details of newer methods being developed to quantify these constituents will be presented.

The Size Exclusion Characteristics of Type I Collagen

The mineral in bone is located primarily within the collagen fibril, and during mineralization the fibril is formed first and then water within the fibril is replaced with mineral. The collagen fibril therefore provides the aqueous compartment in which mineral grows. Although knowledge of the size of molecules that can diffuse into the fibril to affect crystal growth is critical to understanding the mechanism of bone mineralization, there have been as yet no studies on the size exclusion properties of the collagen fibril. To determine the size exclusion characteristics of collagen, we developed a gel filtration-like procedure that uses columns containing collagen from tendon and bone. The elution volumes of test molecules show the volume within the packed column that is accessible to the test molecules, and therefore reveal the size exclusion characteristics of the collagen within the column. These experiments show that molecules smaller than a 6-kDa protein diffuse into all of the water within the collagen fibril, whereas molecules larger than a 40-kDa protein are excluded from this water. These studies provide an insight into the mechanism of bone mineralization. Molecules and apatite crystals smaller than a 6-kDa protein can diffuse into all water within the fibril and so can directly impact mineralization. Although molecules larger than a 40-kDa protein are excluded from the fibril, they can initiate mineralization by forming small apatite crystal nuclei that diffuse into the fibril, or can favor fibril mineralization by inhibiting apatite growth everywhere but within the fibril.

Platelet receptor recognition and cross-talk in collagen-induced activation of platelets

Comprehensive mapping of protein-binding sites within human collagen III has allowed the recognition motifs for integrin alpha(2)beta(1) and VWF A3 domain to be identified. Glycoprotein VI-binding sites are understood, although less well defined. This information, together with recent developments in understanding collagen fiber architecture, and crystal structures of the receptor collagen-binding domains, allows a coherent model for the interaction of collagen with the platelet surface to be developed. This complements our understanding of the orchestration of receptor presentation by membrane microdomains, such that the polyvalent collagen surface may stabilize signaling complexes within the heterogeneous receptor composition of the lipid raft. The ensuing interactions lead to the convergence of signals from each of the adhesive receptors, mediated by FcR gamma-chain and/or FcgammaRIIa, leading to concerted and co-operative platelet activation. Each receptor has a shear-dependent role, VWF/GpIb essential at high shear, and alpha(2)beta(1) at low and intermediate shear, whilst GpVI provides core signals that contribute to enhanced integrin affinity, tighter binding to collagen and consequent platelet activation.

The variability in type I collagen helical pitch is reflected in the D periodic fibrillar structure

The variability in amino acid axial rise per residue of the collagen helix is a potentially important parameter that is missing in many structural models of fibrillar collagen to date. The significance of this variability has been supported by evidence from collagen axial structures determined by electron microscopy and X-ray diffraction, as well as studies of the local sequence-dependent conformation of the collagen helix. Here, sequence-dependent variation of the axial rise per residue was used to improve the fit between simulated diffraction patterns derived from model structures of the axially projected microfibrillar structure and the observed X-ray diffraction pattern from hydrated rat tail tendon. Structural models were adjusted using a genetic algorithm that allowed a wide range of structures to be tested efficiently. The results show that variation of the axial rise per residue could reduce the difference metric between model and observed data by up to 50%, indicating that such a variable is a necessary part of fibril model structure building. The variation in amino acid translation was also found to be influenced by the number of proline and hydroxyproline residues in the triple helix structure.

Creating ultrathin nanoscopic collagen matrices for biological and biotechnological applications

The biofunctionalization of materials creates interfaces on which proteins, cells, or tissues can fulfill native or desired tasks. Here we report how to control the assembly of type I collagen into well-defined nanoscopic matrices of different patterns. Collagen fibrils in these ultrathin (approximately 3 nm) matrices maintained their native structure as observed in vivo. This opens up the possibility to create programmable biofunctionalized matrices using collagen-binding proteins or proteins fused with collagen-binding domains. Applied to eukaryotic cells, these nanostructured matrices can direct cellular processes such as adhesion, orientation and migration.

Micromechanical bending of single collagen fibrils using atomic force microscopy

A new micromechanical technique was developed to study the mechanical properties of single collagen fibrils. Single collagen fibrils, the basic components of the collagen fiber, have a characteristic highly organized structure. Fibrils were isolated from collagenous materials and their mechanical properties were studied with atomic force microscopy (AFM). In this study, we determined the Young's modulus of single collagen fibrils at ambient conditions from bending tests after depositing the fibrils on a poly(dimethyl siloxane) (PDMS) substrate containing micro-channels. Force-indentation relationships of freely suspended collagen fibrils were determined by loading them with a tip-less cantilever. From the deflection-piezo displacement curve, force-indentation curves could be deduced. With the assumption that the behavior of collagen fibrils can be described by the linear elastic theory of isotropic materials and that the fibrils are freely supported at the rims, a Young's modulus of 5.4 +/- 1.2 GPa was determined. After cross-linking with glutaraldehyde, the Young's modulus of a single fibril increases to 14.7 +/- 2.7 GPa. When it is assumed that the fibril would be fixed at the ends of the channel the Young's moduli of native and cross-linked collagen fibrils are calculated to be 1.4 +/- 0.3 GPa and 3.8 +/- 0.8 GPa, respectively. The minimum and maximum values determined for native and glutaraldehyde cross-linked collagen fibrils represent the boundaries of the Young's modulus.

A model for biased diffusion of collagenase along collagen fibrils

We present a model to describe the biased diffusion of a collagenase along collagen fibrils. Based on the structures of collagen fibril and collagenase, the interaction is described by a one-dimensional potential that is symmetric in the region of no cleavage and asymmetric in the cleavage region. We show that the mean velocity of the unidirectional diffusion of the collagenase depends on the three parameters: the asymmetric ratio of the local potential in the cleavage region, the chemical reaction rate of proteolysis and the jumping rate of collagenase between two neighboring tracks. We calculate the correlation function and the mean transport velocity for both wild-type and mutant collagenases along collagen fibrils, the results of which are consistent with the previous experiments.

Microfibrillar structure of type I collagen in situ

The fibrous collagens are ubiquitous in animals and form the structural basis of all mammalian connective tissues, including those of the heart, vasculature, skin, cornea, bones, and tendons. However, in comparison with what is known of their production, turnover and physiological structure, very little is understood regarding the three-dimensional arrangement of collagen molecules in naturally occurring fibrils. This knowledge may provide insight into key biological processes such as fibrillo-genesis and tissue remodeling and into diseases such as heart disease and cancer. Here we present a crystallographic determination of the collagen type I supermolecular structure, where the molecular conformation of each collagen segment found within the naturally occurring crystallographic unit cell has been defined (P1, a approximately 40.0 A, b approximately 27.0 A, c approximately 678 A, alpha approximately 89.2 degrees , beta approximately 94.6 degrees , gamma approximately 105.6 degrees ; reflections: 414, overlapping, 232, and nonoverlapping, 182; resolution, 5.16 A axial and 11.1 A equatorial). This structure shows that the molecular packing topology of the collagen molecule is such that packing neighbors are arranged to form a supertwisted (discontinuous) right-handed microfibril that interdigitates with neighboring microfibrils. This interdigitation establishes the crystallographic superlattice, which is formed of quasihexagonally packed collagen molecules. In addition, the molecular packing structure of collagen shown here provides information concerning the potential modes of action of two prominent molecules involved in human health and disease: decorin and the Matrix Metallo-Proteinase (MMP) collagenase.

Molecular dynamics study of onset of water gelation around the collagen triple helix

The onset of water gelation around a collagen-like triple helix peptide was studied at ambient temperature and pressure by performing Molecular Dynamics simulations. The radial distribution functions of the oxygen and hydrogen atoms of water are distorted below 4 A from the peptide. The distortion is accompanied by the breakdown of the tetrahedral coordination of the hydrogen-bonded network of water molecules. The water shell around the peptide consists of alternating regions of higher and lower density. In agreement with experiments we find that the first hydration shell is kinetically labile, with a residence time in the order of picoseconds for a water molecule. From the computed diffusion coefficient, a key measure of the collective dynamics, we estimate the average diffusion speed decreases by a factor of 1.5 close to the peptide compared to the liquid. Our results give new insight in gel formation and structure on a molecular level.

Observing growth steps of collagen self-assembly by time-lapse high-resolution atomic force microscopy

Insights into molecular mechanisms of collagen assembly are important for understanding countless biological processes and at the same time a prerequisite for many biotechnological and medical applications. In this work, the self-assembly of collagen type I molecules into fibrils could be directly observed using time-lapse atomic force microscopy (AFM). The smallest isolated fibrillar structures initiating fibril growth showed a thickness of approximately 1.5 nm corresponding to that of a single collagen molecule. Fibrils assembled in vitro established an axial D-periodicity of approximately 67 nm such as typically observed for in vivo assembled collagen fibrils from tendon. At given collagen concentrations of the buffer solution the fibrils showed constant lateral and longitudinal growth rates. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Their thickness of approximately 3 nm suggests that the fibrils were build from laterally assembled collagen microfibrils. Laterally the fibrils grew in steps of approximately 4 nm, indicating microfibril formation and incorporation. Thus, we suggest collagen fibrils assembling in a two-step process. In a first step, collagen molecules assemble with each other. In the second step, these molecules then rearrange into microfibrils which form the building blocks of collagen fibrils. High-resolution AFM topographs revealed substructural details of the D-band architecture of the fibrils forming the collagen matrix. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy.

Water in tendon: orientational analysis of the free induction decay

The orientation dependence of the free induction decay (FID) of 1H NMR water signal in ex vivo bovine digital flexor tendon at the native level of hydration is reported. Residual dipolar coupling due to the overall tissue anisotropy produces a 6:1 change in the signal intensity as an angle between the long axis of a specimen and the external magnetic field is changed from the "magic angle" of 54.7 degrees to 0 degrees. The strength of residual dipolar interactions between water protons was estimated by orientational analysis of the signal intensity to be equal to 780 Hz. Apparent signal maxima are observed at orientations 8-13 degrees away from 54.7 degrees due to an inhomogeneous contribution to the decay. A small fraction of total water in tendon is detectable at all orientations and exhibits a shift in the precession frequency. It is hypothesized that this water fraction resides in the interconnecting gaps at the ends of collagen molecules. The gaps have a disordered environment that allows for a zero time average of dipolar interactions. Measured frequency and phase shifts are interpreted as signatures of the bulk magnetic susceptibility effect due to geometry of the cavity formed by adjacent gaps at the ends of the collagen molecules. The multiexponentiality of the FID decay is hypothesized to be due to the exchange between orientationally restricted water structured along the length of the collagen molecule and disordered water in the cavity.

A novel microstructural approach in tendon viscoelastic modelling at the fibrillar level

Novel applications in rehabilitation, surgery and tissue engineering require the knowledge of the mechanical behaviour of the tissues at microstructural level. The aim of this work is to investigate the viscoelastic properties of the tendon from the interaction of its biological constituents in the fibrillar network. Traction, relaxation and creep in-vitro tests have been performed on porcine flexor digital tendons. A viscoelastic constitutive equation at finite deformation is presented. The fibrillar deformation modes are described through a network of adaptive links between collagen type I and decorin. The theoretical predictions fit accurately the experimental data. The results of the model demonstrate the mechanical importance of glycosaminoglycan chains of decorin for the differential recruitment and the activation of fibrillar collagen.

Elastic properties, Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics

The aim of this report is to investigate at microscopic level the elastic properties of a tropocollagen-like molecule submitted to linear traction along its longitudinal axis. For this purpose, we performed steered molecular dynamics (SMD) simulations for a wide range of spring constants in order to test the molecular response based on a two-spring model connected in series. An elastic behavior was observed in an elongation range of 2.5-4% of the molecular length, estimating an "effective molecular elastic constant" of 1.02+/-0.20 kcal/mol A2 in this region. Accordingly, a Young's modulus for the tropocollagen molecule of Y=4.8+/-1.0 GPa was calculated. The complex hydrogen bond network was traced along molecular dynamics (MD) and SMD simulations revealing a rearrangement of these interactions preserving the integrity of the molecular structure when submitted to traction. No evidence of the significant role attributed to water bridges for structural stability was detected, on the contrary facts pointed out that the hydrogen bond network might be the responsible.

Molecular-scale Topographic Cues Induce the Orientation and Directional Movement of Fibroblasts on Two-dimensional Collagen Surfaces

Collagen fibres within the extracellular matrix lend tensile strength to tissues and form a functional scaffold for cells. Cells can move directionally along the axis of fibrous structures, in a process important in wound healing and cell migration. The precise nature of the structural cues within the collagen fibrils that can direct cell movement are not known. We have investigated the structural features of collagen that are required for directional motility of mouse dermal fibroblasts, by analysing cell movement on two-dimensional collagen surfaces. The surfaces were prepared with aligned fibrils of collagen type I, oriented in a predefined direction. These collagen-coated surfaces were generated with or without the characteristic 67 nm D-periodic banding. Quantitative analysis of cell morphodynamics showed a strong correlation of cell elongation and motional directionality with the orientation of D-periodic collagen microfibrils. Neither directed motility, nor cell body alignment, was observed on aligned collagen lacking D-periodicity, or on D-periodic collagen in the presence of peptide containing an RGD motif. The directional motility of fibroblast cells on aligned collagen type I fibrils cannot be attributed to contact guidance, but requires additional structural information. This allows us to postulate a physiological function for the 67 nm periodicity.

Assembly of collagen into microribbons: effects of pH and electrolytes

Collagen represents the major structural protein of the extracellular matrix. Elucidating the mechanism of its assembly is important for understanding many cell biological and medical processes as well as for tissue engineering and biotechnological approaches. In this work, conditions for the self-assembly of collagen type I molecules on a supporting surface were characterized. By applying hydrodynamic flow, collagen assembled into ultrathin ( approximately 3 nm) highly anisotropic ribbon-like structures coating the entire support. We call these novel collagen structures microribbons. High-resolution atomic force microscopy topographs show that subunits of these microribbons are built by fibrillar structures. The smallest units of these fibrillar structures have cross-sections of approximately 3 x 5nm, consistent with current models of collagen microfibril formation. By varying the pH and electrolyte of the buffer solution during the self-assembly process, the microfibril density and contacts formed within this network could be controlled. Under certain electrolyte compositions the microribbons and microfibers display the characteristic D-periodicity of approximately 65 nm observed for much thicker collagen fibrils. In addition to providing insight into the mechanism of collagen assembly, the ultraflat collagen matrices may also offer novel ways to bio-functionalize surfaces.

Collagen fibril form and function

The majority of collagen in the extracellular matrix is found in a fibrillar form, with long slender filaments each displaying a characteristic approximately 67?nm D-repeat. Here they provide the stiff resilient part of many tissues, where the inherent strength of the collagen triple helix is translated through a number of hierarchical levels to endow that tissue with its specific mechanical properties. A number of collagen types have important structural roles, either comprising the core of the fibril or decorating the fibril surface to give enhanced functionality. The architecture of subfibrillar and suprafibrillar structures (such as microfibrils), lateral crystalline and liquid crystal ordering, interfibrillar interactions, and fibril bundles is described. The fibril surface is recognized as an area that contains a number of intimate interactions between different collagen types and other molecular species, especially the proteoglycans. The interplay between molecular forms at the fibril surface is discussed in terms of their contribution to the regulation of fibril diameter and their role in interfibrillar interactions.

Elastic energy storage in unmineralized and mineralized extracellular matrices (ECMs): a comparison between molecular modeling and experimental measurements

In order to facilitate locomotion and limb movement many animals store energy elastically in their tendons. In the turkey, much of the force generated by the gastrocnemius muscle is stored as elastic energy during tendon deformation and not within the muscle. As limbs move, the tendons are strained causing the collagen fibers in the extracellular matrices to be strained. During growth, avian tendons mineralize in the portions distal to the muscle and show increased tensile strength, modulus, and energy stored per unit strain as a result. In this study the energy stored in unmineralized and mineralized collagen fibers was measured and compared to the amount of energy stored in molecular models. Elastic energy storage values calculated using the molecular model were slightly higher than those obtained from collagen fibers, but display the same increases in slope as the fiber data. We hypothesize that these increases in slope are due to a change from the stretching of flexible regions of the collagen molecule to the stretching of less flexible regions. The elastic modulus obtained from the unmineralized molecular model correlates well with elastic moduli of unmineralized collagen from other studies. This study demonstrates the potential importance of molecular modeling in the design of new biomaterials.

Creating nanoscopic collagen matrices using atomic force microscopy

The atomic force microscope (AFM) is introduced as a biomolecular manipulation machine capable of assembling biological molecules into well-defined molecular structures. Native collagen molecules were mechanically directed into well-defined, two-dimensional templates exhibiting patterns with feature sizes ranging from a few nanometers to several hundreds of micrometers. The resulting nanostructured collagen matrices were only approximately 3-nm thick, exhibited an extreme mechanical stability, and maintained their properties over the time range of several months. Our results directly demonstrate the plasticity of biological assemblies and provide insight into the physical mechanisms by which biological structures may be organized by cells in vivo. These nanoscopic templates may serve as platforms on non-biological surfaces to direct molecular and cellular processes.

Dentin matrix protein 1 immobilized on type I collagen fibrils facilitates apatite deposition in vitro

During bone and dentin mineralization, the crystal nucleation and growth processes are considered to be matrix regulated. Osteoblasts and odontoblasts synthesize a polymeric collagenous matrix, which forms a template for apatite initiation and elongation. Coordinated and controlled reaction between type I collagen and bone/dentin-specific noncollagenous proteins are necessary for well defined biogenic crystal formation. However, the process by which collagen surfaces become mineralized is not understood. Dentin matrix protein 1 (DMP1) is an acidic noncollagenous protein expressed during the initial stages of mineralized matrix formation in bone and dentin. Here we show that DMP1 bound specifically to type I collagen, with the binding region located at the N-telopeptide region of type I collagen. Peptide mapping identified two acidic clusters in DMP1 responsible for interacting with type I collagen. The collagen binding property of these domains was further confirmed by site-directed mutagenesis. Transmission electron microscopy analyses have localized DMP1 in the gap region of the collagen fibrils. Fibrillogenesis assays further demonstrated that DMP1 accelerated the assembly of the collagen fibrils in vitro and also increased the diameter of the reconstituted collagen fibrils. In vitro mineralization studies in the presence of calcium and phosphate ions demonstrated apatite deposition only at the collagen-bound DMP1 sites. Thus specific binding of DMP1 and possibly other noncollagenous proteins on the collagen fibril might be a key step in collagen matrix organization and mineralization.

Three-dimensional reconstructions of extracellular matrix polymers using automated electron tomography

The extracellular matrix is an intricate network of macromolecules which provides support for cells and a framework for tissues. The detailed structure and organisation of most matrix polymers is poorly understood. These polymers have a complex ultrastructure, and it has proved a major challenge both to define their structural organisation and to relate this to their biological function. However, new approaches using automated electron tomography are beginning to reveal important insights into the molecular assembly and structural organisation of two of the most abundant polymer systems in the extracellular matrix. We have generated three-dimensional reconstructions of collagen fibrils from bovine cornea and fibrillin microfibrils from ciliary zonules. Analysis of these data has provided new insights into the organisation and function of these large macromolecular assemblies.

Building collagen molecules, fibrils, and suprafibrillar structures

Fibril-forming collagens are synthesized in precursor form, procollagens, with N- and C-terminal propeptide extensions. The C-propeptides direct chain association during intracellular assembly of the procollagen molecule from its three constituent polypeptide chains. Following or during secretion into the extracellular matrix, propeptides are cleaved by specific procollagen proteinases, thereby triggering fibril formation. The recent determination of the low-resolution structure of the C-propeptide trimer gives insights into the mechanism of procollagen chain association. In the extracellular matrix, the procollagen C-propeptides ensure procollagen solubility, while persistence of the N-propeptides controls fibril shape. Mechanisms for the control of fibril diameter are reviewed in terms of the radial packing model for collagen fibril structure. Finally, procollagen molecules have recently been shown to undergo liquid crystalline ordering in solution, prior to fibril assembly. This may provide an explanation for the liquid crystal-like suprafibrillar architectures of different connective tissues.