Compressed microfibril models of the native collagen fibril

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.

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.

Fibril growth kinetics link buffer conditions and topology of 3D collagen I networks

Three-dimensional fibrillar networks reconstituted from collagen I are widely used as biomimetic scaffolds for in vitro and in vivo cell studies. Various physicochemical parameters of buffer conditions for in vitro fibril formation are well known, including pH-value, ion concentrations and temperature. However, there is a lack of a detailed understanding of reconstituting well-defined 3D network topologies, which is required to mimic specific properties of the native extracellular matrix. We screened a wide range of relevant physicochemical buffer conditions and characterized the topology of the reconstituted 3D networks in terms of mean pore size and fibril diameter. A congruent analysis of fibril formation kinetics by turbidimetry revealed the adjustment of the lateral growth phase of fibrils by buffer conditions to be key in the determination of pore size and fibril diameter of the networks. Although the kinetics of nucleation and linear growth phase were affected by buffer conditions as well, network topology was independent of those two growth phases. Overall, the results of our study provide necessary insights into how to engineer 3D collagen matrices with an independent control over topology parameters, in order to mimic in vivo tissues in in vitro experiments and tissue engineering applications.

STATEMENT OF SIGNIFICANCE

The study reports a comprehensive analysis of physicochemical conditions of buffer solutions to reconstitute defined 3D collagen I matrices. By a combined analysis of network topology, i.e., pore size and fibril diameter, and the kinetics of fibril formation we can reveal the dependence of 3D network topology on buffer conditions, such as pH-value, phosphate concentration and sodium chloride content. With those results we are now able to provide engineering strategies to independently tune the topology parameters of widely used 3D collagen scaffolds based on the buffer conditions. By that, we enable the straightforward mimicking of extracellular matrices of in vivo tissues for in vitro cell culture experiments and tissue engineering applications.

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.

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.

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.

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.

Type I collagen D-spacing in fibril bundles of dermis, tendon, and bone: bridging between nano- and micro-level tissue hierarchy

Fibrillar collagens in connective tissues are organized into complex and diverse hierarchical networks. In dermis, bone, and tendon, one common phenomenon at the micrometer scale is the organization of fibrils into bundles. Previously, we have reported that collagen fibrils in these tissues exhibit a 10 nm width distribution of D-spacing values. This study expands the observation to a higher hierarchical level by examining fibril D-spacing distribution in relation to the bundle organization. We used atomic force microscopy imaging and two-dimensional fast Fourier transform analysis to investigate dermis, tendon, and bone tissues. We found that, in each tissue type, collagen fibril D-spacings within a single bundle were nearly identical and frequently differ by less than 1 nm. The full 10 nm range in D-spacing values arises from different values found in different bundles. The similarity in D-spacing was observed to persist for up to 40 μm in bundle length and width. A nested mixed model analysis of variance examining 107 bundles and 1710 fibrils from dermis, tendon, and bone indicated that fibril D-spacing differences arise primarily at the bundle level (∼76%), independent of species or tissue types.

Nanoscale structure of type I collagen fibrils: quantitative measurement of D-spacing

This article details a quantitative method to measure the D-periodic spacing of type I collagen fibrils using atomic force microscopy coupled with analysis using a two-dimensional fast fourier transform approach. Instrument calibration, data sampling and data analysis are discussed and comparisons of the data to the complementary methods of electron microscopy and X-ray scattering are made. Examples of the application of this new approach to the analysis of type I collagen morphology in disease models of estrogen depletion and osteogenesis imperfecta (OI) are provided. We demonstrate that it is the D-spacing distribution, not the D-spacing mean, that showed statistically significant differences in estrogen depletion associated with early stage osteoporosis and OI. The ability to quantitatively characterize nanoscale morphological features of type I collagen fibrils will provide important structural information regarding type I collagen in many research areas, including tissue aging and disease, tissue engineering, and gene knockout studies. Furthermore, we also envision potential clinical applications including evaluation of tissue collagen integrity under the impact of diseases or drug treatments.

Mapping structural landmarks, ligand binding sites, and missense mutations to the collagen IV heterotrimers predicts major functional domains, novel interactions, and variation in phenotypes in inherited diseases affecting basement membranes

Collagen IV is the major protein found in basement membranes. It comprises three heterotrimers (α1α1α2, α3α4α5, and α5α5α6) that form distinct networks, and are responsible for membrane strength and integrity.We constructed linear maps of the collagen IV heterotrimers ("interactomes") that indicated major structural landmarks, known and predicted ligand-binding sites, and missense mutations, in order to identify functional and disease-associated domains, potential interactions between ligands, and genotype–phenotype relationships. The maps documented more than 30 known ligand-binding sites as well as motifs for integrins, heparin, von Willebrand factor (VWF), decorin, and bone morphogenetic protein (BMP). They predicted functional domains for angiogenesis and haemostasis, and disease domains for autoimmunity, tumor growth and inhibition, infection, and glycation. Cooperative ligand interactions were indicated by binding site proximity, for example, between integrins, matrix metalloproteinases, and heparin. The maps indicated that mutations affecting major ligand-binding sites, for example, for Von Hippel Lindau (VHL) protein in the α1 chain or integrins in the α5 chain, resulted in distinctive phenotypes (Hereditary Angiopathy, Nephropathy, Aneurysms, and muscle Cramps [HANAC] syndrome, and early-onset Alport syndrome, respectively). These maps further our understanding of basement membrane biology and disease, and suggest novel membrane interactions, functions, and therapeutic targets.

Functional biomimetic analogs help remineralize apatite-depleted demineralized resin-infiltrated dentin via a bottom-up approach

Natural biominerals are formed through metastable amorphous precursor phases via a bottom-up, nanoparticle-mediated mineralization mechanism. Using an acid-etched human dentin model to create a layer of completely demineralized collagen matrix, a bio-inspired mineralization scheme has been developed based on the use of dual biomimetic analogs. These analogs help to sequester fluidic amorphous calcium phosphate nanoprecursors and function as templates for guiding homogeneous apatite nucleation within the collagen fibrils. By adopting this scheme for remineralizing adhesive resin-bonded, completely demineralized dentin, we have been able to redeposit intrafibrillar and extrafibrillar apatites in completely demineralized collagen matrices that are imperfectly infiltrated by resins. This study utilizes a spectrum of completely and partially demineralized dentin collagen matrices to further validate the necessity for using a biomimetic analog-containing medium for remineralizing resin-infiltrated partially demineralized collagen matrices in which remnant seed crystallites are present. In control specimens in which biomimetic analogs are absent from the remineralization medium, remineralization could only be seen in partially demineralized collagen matrices, probably by epitaxial growth via a top-down crystallization approach. Conversely, in the presence of biomimetic analogs in the remineralization medium, intrafibrillar remineralization of completely demineralized collagen matrices via a bottom-up crystallization mechanism can additionally be identified. The latter is characterized by the transition of intrafibrillar minerals from an inchoate state of continuously braided microfibrillar electron-dense amorphous strands to discrete nanocrystals, and ultimately into larger crystalline platelets within the collagen fibrils. Biomimetic remineralization via dual biomimetic analogs has the potential to be translated into a functional delivery system for salvaging failing resin-dentin bonds.

Elastic energy storage in an unmineralized collagen type I molecular model with explicit solvation and water infiltration

Collagen type I is a structural protein that provides tensile strength to tendons and ligaments. Type I collagen molecules form collagen fibers, which are viscoelastic and can therefore store energy elastically via molecular elongation and dissipate viscous energy through molecular rearrangement and fibrillar slippage. The ability to store elastic energy is important for the resiliency of tendons and ligaments, which must be able to deform and revert to their initial lengths with changes in load. In an earlier paper by one of the present authors, molecular modeling was used to investigate the role of mineralization upon elastic energy storage in collagen type I. Their collagen model showed a similar trend to their experimental data but with an over-estimation of elastic energy storage. Their simulations were conducted in vacuum and employed a distance-dependent dielectric function. In this study, we performed a re-evaluation of Freeman and Silver's model data incorporating the effects of explicit solvation and water infiltration, in order to determine whether the model data could be improved with a more accurate representation of the solvent and osmotic effects. We observed an average decrease in the model's elastic energy storage of 45.1%+/-6.9% in closer proximity to Freeman and Silver's experimental data. This suggests that although the distance-dependent dielectric implicit solvation approach was favored for its increased speed and decreased computational requirements, an explicit representation of water may be necessary to more accurately model solvent interactions in this particular system. In this paper, we discuss the collagen model described by Freeman and Silver, the present model building approach, the application of the present model to that of Freeman and Silver, and additional assumptions and limitations.

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.

Nanoscale scraping and dissection of collagen fibrils

The main function of collagen is mechanical, hence there is a fundamental scientific interest in experimentally investigating the mechanical and structural properties of collagen fibrils on the nanometre scale. Here, we present a novel atomic force microscopy (AFM) based scraping technique that can dissect the outer layer of a biological specimen. Applied to individual collagen fibrils, the technique was successfully used to expose the fibril core and reveal the presence of a D-banding-like structure. AFM nanoindentation measurements of fibril shell and core indicated no significant differences in mechanical properties such as stiffness (reduced modulus), hardness, adhesion and adhesion work. This suggests that collagen fibrils are mechanically homogeneous structures. The scraping technique can be applied to other biological specimens, as demonstrated on the example of bacteria.

COMP acts as a catalyst in collagen fibrillogenesis

We have previously reported that COMP (cartilage oligomeric matrix protein) is prominent in cartilage but is also present in tendon and binds to collagens I and II with high affinity. Here we show that COMP influences the fibril formation of these collagens. Fibril formation in the presence of pentameric COMP was much faster, and the amount of collagen in fibrillar form was markedly increased. Monomeric COMP, lacking the N-terminal coiled-coil linker domain, decelerated fibrillogenesis. The data show that stimulation of collagen fibrillogenesis depends on the pentameric nature of COMP and not only on collagen binding. COMP interacts primarily with free collagen I and II molecules, bringing several molecules to close proximity, apparently promoting further assembly. These assemblies further join in discrete steps to a narrow distribution of completed fibril diameters of 149 +/- 16 nm with a banding pattern of 67 nm. COMP is not found associated with the mature fibril and dissociates from the collagen molecules or their early assemblies. However, a few COMP molecules are found bound to more loosely associated molecules at the tip/end of the growing fibril. Thus, COMP appears to catalyze the fibril formation by promoting early association of collagen molecules leading to increased rate of fibrillogenesis and more distinct organization of the fibrils.

Mechanical properties of collagen fibrils

The formation of collagen fibers from staggered subfibrils still lacks a universally accepted model. Determining the mechanical properties of single collagen fibrils (diameter 50-200 nm) provides new insights into collagen structure. In this work, the reduced modulus of collagen was measured by nanoindentation using atomic force microscopy. For individual type 1 collagen fibrils from rat tail, the modulus was found to be in the range from 5 GPa to 11.5 GPa (in air and at room temperature). The hypothesis that collagen anisotropy is due to the subfibrils being aligned along the fibril axis is supported by nonuniform surface imprints performed by high load nanoindentation.

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.

Type I collagen N-Telopeptides adopt an ordered structure when docked to their helix receptor during fibrillogenesis*

The in vitro rate and specificity of fibrillogenesis in type I collagen depends on the integrity of the amino (N)-telopeptide domain. In vivo an intact N-telopeptide domain is also required for normal fibril assembly. Although Chou-Fasman predictions and NMR studies suggested that a type I beta-turn could be induced in alpha1(I) N-telopeptide chains, computer modeling did not identify ordered structures. Nevertheless, X-ray analysis and electron tomography studies have shown that the N-telopeptide is in one of the most highly ordered fibril domains. This study was undertaken to determine if the docking of the N-telopeptide to its helix receptor domain could induce the telopeptides to take up a specific conformation. With use of molecular modeling suite of programs, a (Gly-Pro-Pro)(n) triple-helical structure was built on the basis of high-resolution X-ray crystallographic coordinates and then replaced with the actual bovine collagen residues 924-938, the triple-helical alpha1(I)-N-telopeptide-receptor sequences. Energy minimization produced a modified triple-helical conformation. The bovine alpha1(I) N-telopeptide sequence was similarly minimized and docked to this receptor. The docking induced an ordered conformation with a stabilizing hydrogen bond in the N-telopeptide and, importantly, a reciprocal reordering of the triple-helical conformation in the binding domain. This docked structure placed Lys residues in both telopeptide and helix in the correct locations for cross-link formation. The modeling has been extended to the three-chain N-telopeptide domain and finally to the construction of the Hulmes-Miller quasi-hexagonal packing structure. Each N-telopeptide domain can form linkages with two adjacent, aligned helix receptor domains. The telopeptides and the order of staggering of the three chains in the helix play crucial roles in the packing and intrafibrillar cross-linking patterns and the relative azimuthal orientations of adjacent molecules in the fibril. The models confirm the high order in the N-telopeptide 4D overlap zone.

Assembly of collagen types II, IX and XI into nascent hetero-fibrils by a rat chondrocyte cell line

The cell line, RCS-LTC (derived from the Swarm rat chondrosarcoma), deposits a copious extracellular matrix in which the collagen component is primarily a polymer of partially processed type II N-procollagen molecules. Transmission electron microscopy of the matrix shows no obvious fibrils, only a mass of thin unbanded filaments. We have used this cell system to show that the type II N-procollagen polymer nevertheless is stabilized by pyridinoline cross-links at molecular sites (mediated by N- and C-telopeptide domains) found in collagen II fibrils processed normally. Retention of the N-propeptide therefore does not appear to interfere with the interactions needed to form cross-links and mature them into trivalent pyridinoline residues. In addition, using antibodies that recognize specific cross-linking domains, it was shown that types IX and XI collagens, also abundantly deposited into the matrix by this cell line, become covalently cross-linked to the type II N-procollagen. The results indicate that the assembly and intertype cross-linking of the cartilage type II collagen heteropolymer is an integral, early process in fibril assembly and can occur efficiently prior to the removal of the collagen II N-propeptides.

Investigations into the polymorphism of rat tail tendon fibrils using atomic force microscopy

Collagen type I displays a typical banding periodicity of 67 nm when visualized by atomic force or transmission electron microscopy imaging. We have investigated collagen fibers extracted from rat tail tendons using atomic force microscopy, under different ionic and pH conditions. The majority of the fibers reproduce the typical wavy structure with 67 nm spacing and a height difference between the peak and the grooves of at least 5 nm. However, we were also able to individuate two other banding patterns with 23+/-2 nm and 210+/-15 nm periodicities. The small pattern showed height differences of about 2 nm, whereas the large pattern seems to be a superposition of the 67 nm periodicity showing height differences of about 20 nm. Furthermore, we could show that at pH values of 3 and below the fibril structure gets dissolved whereas high concentrations of NaCl and CaCl(2) could prevent this effect.

Hierarchical structures in fibrillar collagens

The collagen family includes several large transcripts, usually exceeding 1000 amino acid residues per single chain. As a group, they make up 1/3 of all the protein of the body and are responsible for modelling the framework of connective tissues; individually, they show both a wide variety and a complex hierarchy of mutual interactions, and form a range of functional aggregates including a variety of fibrils, microfibrils and basal membranes. Of the collagens, the fibril-forming types (i.e. the types I, II III, V and XI) are the most abundant and the most extensively studied. At the primary structure level, the amino acid sequence of all collagens is now known in detail and it shows a distinctive domain organization, its composition being dominated by the amino acid glycine (roughly 1/3 of all residues) and by post-translational hydroxylation of proline and lysine residues. Collagen secondary and tertiary structure, which together give origin to a classic triple helix, were painstakingly determined in the 1950s and 1960s. In contrast with the primary, secondary and tertiary structure, the supramolecular arrangement within collagen fibres seems to be far more elusive, and none of the models so far advanced can be said to be universally accepted. Half a century of research and debate spawned numerous mutually incompatible models, most of them focussing either on a quasi-crystalline supramolecular array or on several forms of microfibrillar aggregates, while radial fibrils, epitaxial fibrils and other structural models have almost been ignored. In many cases, data gained with a single technique from a single tissue were arbitrarily given a general legitimacy, whilst other well-documented morphological evidence went virtually unnoticed by the scientific community.Moreover, in recent years there has been a growing interest in the multiple interactions of collagens with the other macromolecules of the extra-cellular matrix, as their structure and their functional role become known. It is now indisputable that collagen interacts and forms functional entities with several other macromolecules of the extracellual matrix. This paper will succinctly review some current concepts on the structural biology of collagen higher-order structures.

Mapping the ligand-binding sites and disease-associated mutations on the most abundant protein in the human, type I collagen

Type I collagen is the most abundant protein in humans, and it helps to maintain the integrity of many tissues via its interactions with cell surfaces, other extracellular matrix molecules, and growth and differentiation factors. Nearly 50 molecules have been found to interact with type I collagen, and for about half of them, binding sites on this collagen have been elucidated. In addition, over 300 mutations in type I collagen associated with human connective tissue disorders have been described. However, the spatial relationships between the known ligand-binding sites and mutation positions have not been examined. To this end, here we have created a map of type I collagen that includes all of its ligand-binding sites and mutations. The map reveals the existence of several hot spots for ligand interactions on type I collagen and that most of the binding sites locate to its C-terminal half. Moreover, on the collagen fibril some potentially relevant relationships between binding sites were observed including the following: fibronectin- and certain integrin-binding regions are near neighbors, which may mechanistically relate to fibronectin-dependent cell-collagen attachment; proteoglycan binding may potentially impact upon collagen fibrillogenesis, cell-collagen attachment, and collagen glycation seen in diabetes and aging; and mutations associated with osteogenesis imperfecta and other disorders show apparently nonrandom distribution patterns within both the monomer and fibril, implying that mutation positions correlate with disease phenotype. These and other observations presented here may provide novel insights into evaluating type I collagen functions and the relationships between its binding partners and mutations.

Collagen packing and mineralization. An x-ray scattering investigation of turkey leg tendon

Several recent results are suggesting that the collagen packing in mineralized tissues is much less regular than in the case of other nonmineralizing collagen, e.g., rat tail tendon. To clarify this question we have investigated the molecular arrangement in mineralized and unmineralized turkey leg tendon as a model for the collagen of mineralized tissues. Using a combination of diffuse x-ray scattering and computer simulation, it could be shown quantitatively that, although the collagen fibril structure is periodic in the axial direction, it is similar to a two-dimensional fluid in the lateral plane. This has important consequences for the understanding of the mineralization process, which is also discussed.

Analysis of the calcium distribution in predentine by EELS and of the early crystal formation in dentine by ESI and ESD

Predentine is a collagen-rich extracellular matrix between the odontoblasts and the dentine with a width of about 15-20 microns. Electron energy-loss spectroscopy of rat incisors shows a significantly higher calcium content in the predentine at the predentine-dentine border than in the middle region of the predentine. At the predentine-dentine border in the dentine, the calcium and the phosphate groups combine to form apatite crystallites. Electron spectroscopic diffraction with zero-loss filtering revealed that the earliest crystallites contain only Debye-Scherrer rings of apatite, which are fewer in number and more diffuse than the diffraction rings from the mature crystallites. We therefore conclude that the early crystallites still contain lattice defects, which are annealed out to some degree with crystal growth. Electron spectroscopic imaging with zero-loss filtering also showed that the earliest crystallites are chains of dots (or small islands); they build up strands composed of islands, which rapidly acquire a needle-like character and coalesce laterally to form ribbon-or plate-like crystallites. The parallel strands sometimes appear to reinforce the macroperiod of the collagen microfibrils (67 nm) by tiny holes without any crystal-substance lined up perpendicular to the parallel strands of the crystallites.

Molecular packing in type I collagen fibrils. A model with neighbouring collagen molecules aligned in axial register

A detailed stereochemical analysis of intermolecular interactions of collagens made with molecular models and summarized experimental data resulted in a new three-dimensional structural model for collagen fibrils. In this model collagen molecules aligned in axial register form a bunch. The bunches are aligned head to tail and penetrate by 300 A into each other, forming microfibrils; these in turn assemble into fibrils. The new model differs from all the others in that its characteristic axial regularity, with a period of 670 A, results from staggering of the adjacent microfibrils formed by unstaggered molecules rather than from the axial staggering of neighbouring collagen molecules.

Different architectures of the collagen fibril: morphological aspects and functional implications

Several tissues known to contain collagen fibrils with a 'helical' arrangement were studied by t.e.m. and freeze-fracture. In all the tissues examined, the diameter of the collagen fibrils appeared to be tissue-specific and fairly constant within the same tissue. No statistical differences, on the contrary, were detectable in the coiling angle which appeared similar in all the tissues and independent of both diameter and age of the fibril. Rat tail tendon was also examined under the same technical conditions and showed collagen fibrils of large and very heterogeneous diameter and with a consistent 'straight' arrangement. These data seem to suggest that the 'helical' and 'straight' arrangements may actually identify different types of collagen fibrils. The authors discuss the possible functional significance of these arrangements and present two hypotheses on the three-dimensional structure of the 'helical' fibril.

The molecular and fibrillar structure of collagen and its relationship to the mechanical properties of connective tissue

The conformation of type I collagen molecules has been refined using a linked-atom least-squares procedure in conjunction with high-quality X-ray diffraction data. In many tendons these molecules pack in crystalline arrays and a careful measurement of the positions of the Bragg reflections allows the unit cell to be determined with high precision. From a further analysis of the X-ray data it can be shown that the highly ordered overlap region of the collagen fibrils consists of a crystalline array of molecular segments inclined by a small angle with respect to the fibril axis. In contrast, the gap region is less well ordered and contains molecular segments that are likely to be inclined by a similar angle but in a different vertical plane to that found in the overlap region. The collagen molecule thus has a D-periodic crimp in addition to the macroscopic crimp observed visually in the collagen fibres of many connective tissues. The growth and development of collagen fibrils have been studied by electron microscopy for a diverse range of connective tissues and the general pattern of fibril growth has been established as a function of age. In particular, relationships between fibril size distribution, the content and composition of the glycosaminoglycans in the matrix and the mechanical role played by the fibrils in the tissue have been formulated and these now seem capable of explaining many new facets of connective tissue structure and function.

Molecular packing in type I collagen fibrils

Previous studies of the X-ray diffraction pattern of the crystalline regions of type I collagen fibrils yielded information on the unit cell parameters and also the orientation of the pseudo-hexagonally packed molecular segments in the overlap region. The absence of Bragg reflections at high angles attributable to the molecular segments in the gap region led to the suggestion that these segments were more mobile than those in the overlap region. We report a study of the low-angle Bragg reflections in a search for information about the nature of the orientation and packing of the molecular segments in the gap region. We conclude that the (m = 0, n = 0) helix layer plane of the molecular segments in the overlap region makes little or no contribution to the Bragg reflections at low angles, and identify three possible origins for the observed low-angle reflections in the electron density contrast associated with: (1) the "hole" created by the missing molecular segment in the gap region; (2) the telopeptides; or (3) the axial regularities in amino acid residues of a particular type, with periodicities of D/5 or D/6. Sufficient information is available to investigate the first two of these possibilities, and the results obtained suggest specific arrangements for the molecular segments in the overlap and gap regions, and specific connectivities between the molecular segments in successive overlap regions. In addition, we have examined the amino acid sequence and identified features related to the mobility of the molecular segments in the gap region and to the regions where it is thought that molecules are kinked.

Intermolecular cross-linking and stereospecific molecular packing in type I collagen fibrils of the periodontal ligament

A trypsin digest of denatured NaB3H4-reduced native bovine periodontal ligament was prepared and fractionated by gel filtration and cellulose ion-exchange column chromatography. Prior to trypsin digestion, a complete acid hydrolysate was subjected to analyses for nonreducible stable and reducible intermolecular cross-links. Minute amounts of the former and significant amounts of the reduced cross-links dihydroxylysinonorleucine (1.1 mol/mol of collagen), hydroxylysinonorleucine (0.9 mol/mol of collagen), and histidinohydroxymerodesmosine (0.6 mol/mol of collagen) were found. The covalent intermolecular cross-linked two-chained peptides that were isolated were subjected to amino acid and sequence analyses. The structures for the different two-chained linked peptides were alpha 1CB4-5(76-90)[Hyl-87] X alpha 1CB6-(993-22c)[Lysald-16c], alpha 1CB4-5(76-90)[Hyl-87] X alpha 1CB6(993-22c)[Hylald-16c], alpha 2CB4(76-90)[Hyl-87] X alpha 1CB6(993-22c)[Lysald-16c], and alpha 2CB4(76-90)[Hyl-87] X alpha 1CB6(993-22c)[Hylald-16c]. The cross-link in each peptide was glycosylated. This is the first characterization by sequence analysis of a cross-link involving Hyl-87 in an alpha 2 chain in collagen. A stoichiometric conversion of residue 16c aldehyde to an intermolecular cross-link in each of the COOH-terminal nonhelical peptide regions of both alpha 1 chains in a molecule of type I collagen was found. The ratio of alpha 1 to alpha 2 intermolecularly cross-linked chains involved was 3.3:1, indicating a stereospecific three-dimensional molecular packing of type I collagen molecules in bovine periodontal ligament.

Neutron diffraction studies of collagen in fully mineralized bone

Neutron diffraction measurements have been made of the equatorial and meridional spacings of collagen in fully mineralized mature bovine bone and demineralized bone collagen, in both wet and dry conditions. The collagen equatorial spacing in wet mineralized bovine bone is 1.24 nm, substantially lower than the 1.53 nm value observed in wet demineralized bovine bone collagen. Corresponding spacings for dry bone and demineralized bone collagen are 1.16 nm and 1.12 nm, respectively. The collagen meridional long spacing in mineralized bovine bone is 63.6 nm wet and 63.4 nm dry. These data indicate that collagen in fully mineralized bovine bone is considerably more closely packed than had been assumed previously, with a packing density similar to that of the relatively crystalline collagens such as wet rat tail tendon. The data also suggest that less space is available for mineral within the collagen fibrils in bovine bone than had previously been assumed, and that the major portion of the mineral in this bone must be located outside the fibrils.

Packing of collagen molecules modified with 2-propanol

X-ray diffraction data of collagen molecules modified with 2-propanol favour a quasi-hexagonal lateral packing over a quasi-tetragonal one.

Molecular conformation and packing in collagen fibrils

New X-ray diffraction data have been collected from specimens of tendon collagen stained with phosphotungstic acid. Measurements of the positions of the Bragg reflections associated with the crystalline lattice provide, for the first time, a complete description of the unit cell. A strong band of intensity in the molecular transform associated with the pitch of the molecular helix can be identified and a detailed analysis of the intensities and positions of the Bragg reflections in this band has been carried out. The principal conclusions are that the portions of the collagen molecule that contribute to these reflections have a common direction; that they have a length very much less than that of a complete molecule; that the paths of the individual portions through the crystal are incompatible with a completely straight molecule, and that the molecule is therefore crimped. No evidence was obtained for a second series of Bragg reflections attributable to a second set of molecular portions linking the first set, and it is concluded that the linking set is more mobile and subject to positional variation from cell to cell. The most plausible explanation of our finding is that the first set corresponds to the portions of the molecules in the overlap zone and the second set to the portions in the gap zone. A detailed analysis of the Bragg reflections in the strong band of intensity associated with the pitch of the molecular helix has provided information about the relative azimuthal orientations and the lateral positions in the unit cell of the five molecular segments in the overlap zone. None of the existing models for fibril structure accounts satisfactorily for all the results obtained in the present studies and alternative models are developed and tested.

Electron microscopy of argon laser therapy in phakic open-angle glaucoma

In 22 subjects with phakic open-angle glaucoma, trabeculectomies were performed at intervals of three hours to one year after argon laser treatment (ALT). In ten patients the ALT was done with informed consent anticipating that trabeculectomy would be performed at a scheduled time (three hours to two weeks following laser therapy). In 12 other patients, trabeculectomies were required for failure of ALT (one month to one year later). Scanning and transmission electron microscopy of the specimens examined at earlier intervals after laser therapy revealed evidence of heat effects with disruption of trabecular beams, fibrinous material, and necrosis of occasional cells, including melanin-containing endothelial cells, followed by shrinkage of the collagenous components of the trabecular meshwork. The specimens excised at longer intervals after laser treatment showed partial or total occlusion of intertrabecular spaces by a cellular layer of abnormal corneal and/or trabecular endothelial cells with widened cellular interdigitations and numerous prominent filopodial processes typical of migrating cells.

Structure and assembly of the native collagen fibril

Assembly in vitro of the native collagen fibril is a multistep process involving an initial intermediate of unknown structure, linear growth of thin filaments, lateral growth to form the fibril, and stabilization by covalent crosslinks. A model for the structure of the fibril is proposed consisting of a substructure of five-stranded microfibrils laterally compressed to place molecules in cross section on a near-hexagonal lattice.

A molecular model for linear and lateral growth of type I collagen fibrils

A model is proposed for Type I collagen fibrillogenesis in which linear and lateral growth are directed by attractive charged pair interactions. It is suggested that linear growth decreases the rate of rotational motion resulting in an increased rate of lateral collisions. The mechanism of linear aggregation involves interactions between sets of unusual charged pairs located at positions 53, 54 and 56 and positions 990 and 992 as well as in the non-helical ends. These charged pairs attract each other electrostatically as well as form a hydrophobic pocket between the molecules. Lateral growth occurs by attractions between D-staggered, charged pairs which alternate between intra- and interchain states. Interchain interactions lead to lateral association of neighboring molecules and formation of a D-staggered unit containing five trimers. Rotational motion of the triple-helical backbone as well as the ability of charged pairs in their interchain state to interact by several different possible combinations between alpha-chains suggest that lateral packing of collagen molecules into fibrils at least in vitro may not need to be specific.

A new model for packing of type-I collagen molecules in the native fibril

A specific fibril model is presented consisting of bundles of five-stranded microfibrils, which are usually disordered (except axially) but under lateral compression become ordered. The features are as follows (where D = 234 residues or 67 nm): (1) D-staggered collagen molecules 4.5 D long in the helical microfibril have a left-handed supercoil with a pitch of 400-700 residues, but microfibrils need not have helical symmetry. (2) straight-tilted 0.5-D overlap regions on a near-hexagonal lattice contribute the discrete x-ray diffraction reflections arising from lateral order, while the gap regions remain disordered. (3) The overlap regions are equivalent, but are crystallographically distinguished by systematic displacements from the near-hexagonal lattice. (4) The unit cell is the same as in a recently proposed three-dimensional crystal model, and calculated intensities in the equatorial region of the x-ray diffraction pattern agree with observed values.

A mixed packing model for bone collagen

A wide variety of physical properties, including sonic velocity, dimensional changes between wet and dried stages, anisotropy of the tissue properties, density, X-ray diffraction, differential microcalorimetry, dielectric constant, and composition (water, mineral, organic content) for the mineralized and demineralized tissue was used to develop a model for the superlattice structure of bone collagen. A mixed model is suggested where the collagen molecules are in register as in SLS type of aggregation within the microfibril, and the microfibrils are staggered in D unit steps according to the Hodge-Petruska scheme. A square packing model with 4 or more molecules per microfibril best fits the HP scheme with the effective molecular diameter of the wet collagen molecule, and allows for the regular array of axial gap filling microcrystallites of 5 nm or larger diameter. It is concluded that: 1. Macroscopic dimensional changes of adult bovine bone matrix closely match molecular dimensional changes of collagen superlattice. 2. Effective molecular diameter of dry collagen is 1.09 nm and that of wet bone collagen is 1.42-1.45 nm. 3. Water layer of the wet bone collagen molecule is 0.16 nm thick. 4. Water in the bone collagen molecule is distributed in 5 regimes much like in the tendon collagen molecule. 5. "Hidden" water, 0.10 g water per dry collagen of regimes I and II, is within the triple helix. 6. "External" water incorporated in the collagen molecule provides transition between the highly structured collagen molecule and the intermolecular medium. 7. Water incorporated in the mineralized bone collagen molecule is less than in demineralized bone matrix. 8. For adult bovine cortical bone, 25% by volume is water, 32% dry organic, 43% mineral; 28% by volume of the mineral is axial gap filling, 58% radial intrafibrillar, and 14% radial extrafibrillar.

Chemical cross-linking restrictions on models for the molecular organization of the collagen fibre

The nature of the precise packing of collagen molecules into a collagen fibril, producing the characteristic regular banding, is still debatable. The problem has been approached using electron microscopy and X-ray diffraction techniques, and several models have been proposed, including hexagonal packing, an octafibril structure, a two-strand rope and a five-strand rope (for review, see ref. 1). For the past decade the pentafibrillar model, originally proposed by Smith, has been widely accepted as the fundamental building unit. This model, based on the quarter-stagger end-overlap hypothesis of Hodge and Petruska, was supported by the X-ray diffraction data of Miller and Wray. These X-ray data have now been reinterpreted by Hulmes and Miller in terms of a quasi-hexagonal packing of collagen molecules. We argue here that until other characteristic parameters are taken into account, in particular the chemical cross-linking evidence, the packing problem is still unresolved.