Using sequence data to predict the self-assembly of supramolecular collagen structures

Collagen fibrils are the major constituents of the extracellular matrix, which provides structural support to vertebrate connective tissues. It is widely assumed that the superstructure of collagen fibrils is encoded in the primary sequences of the molecular building blocks. However, the interplay between large-scale architecture and small-scale molecular interactions makes the ab initio prediction of collagen structure challenging. Here, we propose a model that allows us to predict the periodic structure of collagen fibers and the axial offset between the molecules, purely on the basis of simple predictive rules for the interaction between amino acid residues. With our model, we identify the sequence-dependent collagen fiber geometries with the lowest free energy and validate the predicted geometries against the available experimental data. We propose a procedure for searching for optimal staggering distances. Finally, we build a classification algorithm and use it to scan 11 data sets of vertebrate fibrillar collagens, and predict the periodicity of the resulting assemblies. We analyzed the experimentally observed variance of the optimal stagger distances across species, and find that these distances, and the resulting fibrillar phenotypes, are evolutionary well preserved. Moreover, we observed that the energy minimum at the optimal stagger distance is broad in all cases, suggesting a further evolutionary adaptation designed to improve the assembly kinetics. Our periodicity predictions are not only in good agreement with the experimental data on collagen molecular staggering for all collagen types analyzed, but also for synthetic peptides. We argue that, with our model, it becomes possible to design tailor-made, periodic collagen structures, thereby enabling the design of novel biomimetic materials based on collagen-mimetic trimers.

Mechanical adaptation of brachiopod shells via hydration-induced structural changes

The function-optimized properties of biominerals arise from the hierarchical organization of primary building blocks. Alteration of properties in response to environmental stresses generally involves time-intensive processes of resorption and reprecipitation of mineral in the underlying organic scaffold. Here, we report that the load-bearing shells of the brachiopod Discinisca tenuis are an exception to this process. These shells can dynamically modulate their mechanical properties in response to a change in environment, switching from hard and stiff when dry to malleable when hydrated within minutes. Using ptychographic X-ray tomography, electron microscopy and spectroscopy, we describe their hierarchical structure and composition as a function of hydration to understand the structural motifs that generate this adaptability. Key is a complementary set of structural modifications, starting with the swelling of an organic matrix on the micron level via nanocrystal reorganization and ending in an intercalation process on the molecular level in response to hydration.

A 43 Ca nuclear magnetic resonance perspective on octacalcium phosphate and its hybrid derivatives

⁴³ Ca nuclear magnetic resonance (NMR) spectroscopy has been extensively applied to the detailed study of octacalcium phosphate (OCP), Ca₈ (HPO₄ )₂ (PO₄ )₄ .5H₂ O, and hybrid derivatives involving intercalated metabolic acids (viz., citrate, succinate, formate, and adipate). Such phases are of importance in the development of a better understanding of bone structure. High-resolution ⁴³ Ca magic angle spinning (MAS) experiments, including double-rotation (DOR) ⁴³ Ca NMR, as well as ⁴³ Ca{¹ H} rotational echo DOR (REDOR) and ³¹ P{⁴³ Ca} REAPDOR NMR spectra, were recorded on a ⁴³ Ca-labeled OCP phase at very high magnetic field (20 T), and complemented by ab initio calculations of NMR parameters using the Gauge-Including Projector Augmented Wave-density functional theory (GIPAW-DFT) method. This enabled a partial assignment of the eight inequivalent Ca²⁺ sites of OCP. Natural-abundance ⁴³ Ca MAS NMR spectra were then recorded for the hybrid organic-inorganic derivatives, revealing changes in the ⁴³ Ca lineshape. In the case of the citrate derivative, these could be interpreted on the basis of computational models of the structure. Overall, this study highlights the advantages of combining high-resolution ⁴³ Ca NMR experiments and computational modeling for studying complex hybrid biomaterials.

Incorporation of nanogels within calcite single crystals for the storage, protection and controlled release of active compounds

Nanocarriers have tremendous potential for the encapsulation, storage and delivery of active compounds. However, current formulations often employ open structures that achieve efficient loading of active agents, but that suffer undesired leakage and instability of the payloads over time. Here, a straightforward strategy that overcomes these issues is presented, in which protein nanogels are encapsulated within single crystals of calcite (CaCO3). Demonstrating our approach with bovine serum albumin (BSA) nanogels loaded with (bio)active compounds, including doxorubicin (a chemotherapeutic drug) and lysozyme (an antibacterial enzyme), we show that these nanogels can be occluded within calcite host crystals at levels of up to 45 vol%. Encapsulated within the dense mineral, the active compounds are stable against harsh conditions such as high temperature and pH, and controlled release can be triggered by a simple reduction of the pH. Comparisons with analogous systems - amorphous calcium carbonate, mesoporous vaterite (CaCO3) polycrystals, and calcite crystals containing polymer vesicles - demonstrate the superior encapsulation performance of the nanogel/calcite system. This opens the door to encapsulating a broad range of existing nanocarrier systems within single crystal hosts for the efficient storage, transport and controlled release of various active guest species.

Poly(ADP-Ribose) Links the DNA Damage Response and Biomineralization

Biomineralization of the extracellular matrix is an essential, regulated process. Inappropriate mineralization of bone and the vasculature has devastating effects on patient health, yet an integrated understanding of the chemical and cell biological processes that lead to mineral nucleation remains elusive. Here, we report that biomineralization of bone and the vasculature is associated with extracellular poly(ADP-ribose) synthesized by poly(ADP-ribose) polymerases in response to oxidative and/or DNA damage. We use ultrastructural methods to show poly(ADP-ribose) can form both calcified spherical particles, reminiscent of those found in vascular calcification, and biomimetically calcified collagen fibrils similar to bone. Importantly, inhibition of poly(ADP-ribose) biosynthesis in vitro and in vivo inhibits biomineralization, suggesting a therapeutic route for the treatment of vascular calcifications. We conclude that poly(ADP-ribose) plays a central chemical role in both pathological and physiological extracellular matrix calcification.

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Poly(ADP-ribose) is found close to ECM calcification in developing bone and arteries

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Poly(ADP-ribose) is produced in response to oxidative stress and delivered to the ECM

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Poly(ADP-ribose) forms dense liquid droplets with calcium ions

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Inhibiting PARP enzyme activity blocks calcification in vitro and in vivo

Pigmentation Chemistry and Radical-Based Collagen Degradation in Alkaptonuria and Osteoarthritic Cartilage

Alkaptonuria (AKU) is a rare disease characterized by high levels of homogentisic acid (HGA); patients suffer from tissue ochronosis: dark brown pigmentation, especially of joint cartilage, leading to severe early osteoarthropathy. No molecular mechanism links elevated HGA to ochronosis; the pigment's chemical identity is still not known, nor how it induces joint cartilage degradation. Here we give key insight on HGA-derived pigment composition and collagen disruption in AKU cartilage. Synthetic pigment and pigmented human cartilage tissue both showed hydroquinone-resembling NMR signals. EPR spectroscopy showed that the synthetic pigment contains radicals. Moreover, we observed intrastrand disruption of collagen triple helix in pigmented AKU human cartilage, and in cartilage from patients with osteoarthritis. We propose that collagen degradation can occur via transient glycyl radicals, the formation of which is enhanced in AKU due to the redox environment generated by pigmentation.

Glycation changes molecular organization and charge distribution in type I collagen fibrils

Collagen fibrils are central to the molecular organization of the extracellular matrix (ECM) and to defining the cellular microenvironment. Glycation of collagen fibrils is known to impact on cell adhesion and migration in the context of cancer and in model studies, glycation of collagen molecules has been shown to affect the binding of other ECM components to collagen. Here we use TEM to show that ribose-5-phosphate (R5P) glycation of collagen fibrils - potentially important in the microenvironment of actively dividing cells, such as cancer cells - disrupts the longitudinal ordering of the molecules in collagen fibrils and, using KFM and FLiM, that R5P-glycated collagen fibrils have a more negative surface charge than unglycated fibrils. Altered molecular arrangement can be expected to impact on the accessibility of cell adhesion sites and altered fibril surface charge on the integrity of the extracellular matrix structure surrounding glycated collagen fibrils. Both effects are highly relevant for cell adhesion and migration within the tumour microenvironment.

Detection of nucleic acids and other low abundance components in native bone and osteosarcoma extracellular matrix by isotope enrichment and DNP-enhanced NMR

Sensitivity enhancement by isotope enrichment and DNP NMR enables detection of minor but biologically relevant species in native intact bone, including nucleic acids, choline from phospholipid headgroups, and histidinyl and hydroxylysyl groups. Labelled matrix from the aggressive osteosarcoma K7M2 cell line confirms the assignments of nucleic acid signals arising from purine, pyrimidine, ribose, and deoxyribose species. Detection of these species is an important and necessary step in elucidating the atomic level structural basis of their functions in intact tissue.

Towards elucidating their biological roles in intact tissue, DNP NMR reveals nucleic acids, and other important low abundance biomolecules in a complex biomaterial, bone, and in cancer extracellular matrix.

Essential but sparse collagen hydroxylysyl post-translational modifications detected by DNP NMR

The sparse but functionally essential post-translational collagen modification 5-hydroxylysine can undergo further transformations, including crosslinking, O-glycosylation, and glycation. Dynamic nuclear polarization (DNP) and stable isotope enriched lysine incorporation provide sufficient solid-state NMR sensitivity to identify these adducts directly in skin and vascular smooth muscle cell extracellular matrix (ECM), without extraction procedures, by comparison with chemical shifts of model compounds. Thus, DNP provides access to the elucidation of structural consequences of collagen modifications in intact tissue.

Solid state NMR - An indispensable tool in organic-inorganic biocomposite characterization; refining the structure of octacalcium phosphate composites with the linear metabolic di-acids succinate and adipate

Octacalcium phosphate (OCP; Ca8(HPO4)2(PO4)4. 5H2O) is a plausible precursor phase of biological hydroxyapatite, which composites with a number of biologically relevant organic metabolites. Widely used material science physicochemical structure determination techniques successfully characterize the mineral component of these composites but leave details of the structure, and interactions with mineral, of the organic component almost completely obscure. The metabolic linear di-acids succinate (SUC) and adipate (ADI) differentially expand the hydrated (100) layer of OCP. 13C13C correlation (proton driven spin diffusion, PDSD) experiments on OCP composited with (U-13C4)-SUC, and (U13C6)-ADI, show that the two di-acids per unit cell adopt non-centrosymmetric but mutually identical structures. 13C{31P}, rotational echo double resonance (REDOR) shows that one end of each linear di-acid is displaced further from the surface of the apatitic OCP layer relative to the other end. Overall the results indicate two di-acids per unit cell disposed perpendicularly across the OCP hydrated layer with one carboxylate of each di-acid substituting a hydrated surface OCP phosphate group. This study re-affirms the unique advantages of ssNMR in elucidating structural details of organic-inorganic biocomposites, and thereby mechanisms underlying the roles of small metabolites in influencing biomineralization mechanisms and outcomes.

Proline provides site-specific flexibility for in vivo collagen

Fibrillar collagens have mechanical and biological roles, providing tissues with both tensile strength and cell binding sites which allow molecular interactions with cell-surface receptors such as integrins. A key question is: how do collagens allow tissue flexibility whilst maintaining well-defined ligand binding sites? Here we show that proline residues in collagen glycine-proline-hydroxyproline (Gly-Pro-Hyp) triplets provide local conformational flexibility, which in turn confers well-defined, low energy molecular compression-extension and bending, by employing two-dimensional ¹³C-¹³C correlation NMR spectroscopy on ¹³C-labelled intact ex vivo bone and in vitro osteoblast extracellular matrix. We also find that the positions of Gly-Pro-Hyp triplets are highly conserved between animal species, and are spatially clustered in the currently-accepted model of molecular ordering in collagen type I fibrils. We propose that the Gly-Pro-Hyp triplets in fibrillar collagens provide fibril "expansion joints" to maintain molecular ordering within the fibril, thereby preserving the structural integrity of ligand binding sites.

Proline provides site-specific flexibility for in vivo collagen

Fibrillar collagens have mechanical and biological roles, providing tissues with both tensile strength and cell binding sites which allow molecular interactions with cell-surface receptors such as integrins. A key question is: how do collagens allow tissue flexibility whilst maintaining well-defined ligand binding sites? Here we show that proline residues in collagen glycine-proline-hydroxyproline (Gly-Pro-Hyp) triplets provide local conformational flexibility, which in turn confers well-defined, low energy molecular compression-extension and bending, by employing two-dimensional ¹³C-¹³C correlation NMR spectroscopy on ¹³C-labelled intact ex vivo bone and in vitro osteoblast extracellular matrix. We also find that the positions of Gly-Pro-Hyp triplets are highly conserved between animal species, and are spatially clustered in the currently-accepted model of molecular ordering in collagen type I fibrils. We propose that the Gly-Pro-Hyp triplets in fibrillar collagens provide fibril "expansion joints" to maintain molecular ordering within the fibril, thereby preserving the structural integrity of ligand binding sites.

Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy

The extracellular matrix of a tissue is as important to life as the cells within it. Its detailed molecular structure defines the environment of a tissue's cells and thus their properties, including differentiation and metabolic status. Collagen proteins are the major component of extracellular matrices. Self-assembled collagen fibrils provide both specific mechanical properties to handle external stresses on tissues and, at the molecular level, well-defined protein binding sites to interact with cells. How the cell-matrix interactions are maintained against the stresses on the tissue is an important and as yet unanswered question. Similarly, how collagen molecular and fibrillar structures change in aging and disease is a crucial open question. Solid-state NMR spectroscopy offers insight into collagen molecular conformation in intact in vivo and in vitro tissues, and in this Account we review how NMR spectroscopy is beginning to provide answers to these questions. In vivo ¹³C,¹⁵N labeling of the extracellular matrix has given insight into collagen molecular dynamics and generated multidimensional NMR "fingerprints" of collagen molecular structure that allow comparison of local collagen conformation between tissues. NMR studies have shown that charged collagen residues (Lys, Arg) adopt extended-side-chain conformations in the fibrillar structure to facilitate charge-charge interactions between neighboring collagen molecules, while hydrophobic residues (Leu, Ile) fold along the collagen molecular axis to minimize the hydrophobic area exposed to surrounding water. Detailed NMR and molecular modeling work has shown that the abundant Gly-Pro-Hyp (Hyp = hydroxyproline) triplets in collagen triple helices confer well-defined flexibility because the proline is conformationally metastable, in contrast to the expectation that these triplets confer structural rigidity. The alignment of the Gly-Pro-Hyp triplets within the fibril structure means that the Gly-Pro-Hyp molecular flexibility generates fibril flexibility. The fibrillar bands of Gly-Pro-Hyp are highly correlated with collagen ligand binding sites, leading to the hypothesis that the fibril alignment of Gly-Pro-Hyp triplets is essential to protect collagen-ligand binding against external stresses on the tissue. Non-enzymatic chemistry between collagen side-chain amine groups (Lys, Arg) and reducing sugars-glycation-is an important source of matrix structural change in aging and disease. Glycation leads to stiffening of collagen fibrils, which is widely speculated to be the result of intermolecular cross-linking. The chemistry of non-enzymatic glycation has been extensively detailed through NMR studies and has been shown to lead to side-chain modifications as the majority reaction products, rather than intermolecular cross-links, with resultant molecular misalignment in the fibrils. Thus, a picture is beginning to emerge in which collagen glycation causes stiffening through misalignment of collagen molecular flexible regions rather than intermolecular cross-linking, meaning that new thinking is needed on how to alleviate collagen structural changes in aging and disease.

Solid state NMR of isotope labelled murine fur: a powerful tool to study atomic level keratin structure and treatment effects

We have prepared mouse fur extensively ¹³C,¹⁵N-labelled in all amino acid types enabling application of 2D solid state NMR techniques which establish covalent and spatial proximities within, and in favorable cases between, residues. ¹³C double quantum-single quantum correlation and proton driven spin diffusion techniques are particularly useful for resolving certain amino acid types. Unlike 1D experiments on isotopically normal material, the 2D methods allow the chemical shifts of entire spin systems of numerous residue types to be determined, particularly those with one or more distinctively shifted atoms such as Gly, Ser, Thr, Tyr, Phe, Val, Leu, Ile and Pro. Also the partial resolution of the amide signals into two signal envelopes comprising of α-helical, and β-sheet/random coil components, enables resolution of otherwise overlapped α-carbon signals into two distinct cross peak families corresponding to these respective secondary structural regions. The increase in resolution conferred by extensive labelling offers new opportunities to study the chemical fate and structural environments of specific atom and amino acid types under the influence of commercial processes, and therapeutic or cosmetic treatments.

Tuning hardness in calcite by incorporation of amino acids

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

Preparation of highly and generally enriched mammalian tissues for solid state NMR

An appreciable level of isotope labelling is essential for future NMR structure elucidation of mammalian biomaterials, which are either poorly expressed, or unexpressable, using micro-organisms. We present a detailed protocol for high level (13)C enrichment even in slow turnover murine biomaterials (fur keratin), using a customized diet supplemented with commercial labelled algal hydrolysate and formulated as a gel to minimize wastage, which female mice consumed during pregnancy and lactation. This procedure produced approximately eightfold higher fur keratin labelling in pups, exposed in utero and throughout life to label, than in adults exposed for the same period, showing both the effectiveness, and necessity, of this approach.

The contribution of solid-state NMR spectroscopy to understanding biomineralization: atomic and molecular structure of bone

Solid-state NMR spectroscopy has had a major impact on our understanding of the structure of mineralized tissues, in particular bone. Bone exemplifies the organic-inorganic composite structure inherent in mineralized tissues. The organic component of the extracellular matrix in bone is primarily composed of ordered fibrils of collagen triple-helical molecules, in which the inorganic component, calcium phosphate particles, composed of stacks of mineral platelets, are arranged around the fibrils. This perspective argues that key factors in our current structural model of bone mineral have come about through NMR spectroscopy and have yielded the primary information on how the mineral particles interface and bind with the underlying organic matrix. The structure of collagen within the organic matrix of bone or any other structural tissue has yet to be determined, but here too, this perspective shows there has been real progress made through application of solid-state NMR spectroscopy in conjunction with other techniques. In particular, NMR spectroscopy has highlighted the fact that even within these structural proteins, there is considerable dynamics, which suggests that one should be cautious when using inherently static structural models, such as those arising from X-ray diffraction analyses, to gain insight into molecular roles. It is clear that the NMR approach is still in its infancy in this area, and that we can expect many more developments in the future, particularly in understanding the molecular mechanisms of bone diseases and ageing.

Collagen labelling with an azide-proline chemical reporter in live cells

Biosynthetic incorporation of an azide-proline chemical reporter into collagen allows selective imaging in live foetal ovine osteoblasts using a strain-promoted [3+2] azide–alkyne cycloaddition reaction.

NMR spectroscopy of native and in vitro tissues implicates polyADP ribose in biomineralization

Nuclear magnetic resonance (NMR) spectroscopy is useful to determine molecular structure in tissues grown in vitro only if their fidelity, relative to native tissue, can be established. Here, we use multidimensional NMR spectra of animal and in vitro model tissues as fingerprints of their respective molecular structures, allowing us to compare the intact tissues at atomic length scales. To obtain spectra from animal tissues, we developed a heavy mouse enriched by about 20% in the NMR-active isotopes carbon-13 and nitrogen-15. The resulting spectra allowed us to refine an in vitro model of developing bone and to probe its detailed structure. The identification of an unexpected molecule, poly(adenosine diphosphate ribose), that may be implicated in calcification of the bone matrix, illustrates the analytical power of this approach.

The effect of particle agglomeration on the formation of a surface-connected compartment induced by hydroxyapatite nanoparticles in human monocyte-derived macrophages

Agglomeration dramatically affects many aspects of nanoparticle–cell interactions. Here we show that hydroxyapatite nanoparticles formed large agglomerates in biological medium resulting in extensive particle uptake and dose-dependent cytotoxicity in human macrophages. Particle citration and/or the addition of the dispersant Darvan 7 dramatically reduced mean agglomerate sizes, the amount of particle uptake and concomitantly cytotoxicity. More surprisingly, agglomeration governed the mode of particle uptake. Agglomerates were sequestered within an extensive, interconnected membrane labyrinth open to the extracellular space. In spite of not being truly intracellular, imaging studies suggest particle degradation occurred within this surface-connected compartment (SCC). Agglomerate dispersion prevented the SCC from forming, but did not completely inhibit nanoparticle uptake by other mechanisms. The results of this study could be relevant to understanding particle–cell interactions during developmental mineral deposition, in ectopic calcification in disease, and during application of hydroxyapatite nanoparticle vectors in biomedicine.

Citrate occurs widely in healthy and pathological apatitic biomineral: mineralized articular cartilage, and intimal atherosclerotic plaque and apatitic kidney stones

There is continuing debate about whether abundant citrate plays an active role in biomineralization of bone. Using solid state NMR dipolar dephasing, we examined another normally mineralized hard tissue, mineralized articular cartilage, as well as biocalcifications arising in pathological conditions, mineralized intimal atherosclerotic vascular plaque, and apatitic uroliths (urinary stones). Residual nondephasing ¹³C NMR signal at 76 ppm in the spectra of mineralized cartilage and vascular plaque indicates that a quaternary carbon atom resonates at this frequency, consistent with the presence of citrate. The presence, and as yet unproven possible mechanistic involvement, of citrate in tissue mineralization extends the compositional, structural, biogenetic, and cytological similarities between these tissues and bone itself. Out of 10 apatitic kidney stones, five contained NMR-detectable citrate. Finding citrate in a high proportion of uroliths may be significant in view of the use of citrate in urolithiasis therapy and prophylaxis. Citrate may be essential for normal biomineralization (e.g., of cartilage), play a modulatory role in vascular calcification which could be a target for therapeutic intervention, and drive the formation of apatitic rather than other calcific uroliths, including more therapeutically intractable forms of calcium phosphate.

Applications of NMR crystallography to problems in biomineralization: refinement of the crystal structure and 31P solid-state NMR spectral assignment of octacalcium phosphate

By combining X-ray crystallography, first-principles density functional theory calculations, and solid-state nuclear magnetic resonance spectroscopy, we have refined the crystal structure of octacalcium phosphate (OCP), reassigned its (31)P NMR spectrum, and identified an extended hydrogen-bonding network that we propose is critical to the structural stability of OCP. Analogous water networks may be related to the critical role of the hydration state in determining the mechanical properties of bone, as OCP has long been proposed as a precursor phase in bone mineral formation. The approach that we have taken in this paper is broadly applicable to the characterization of crystalline materials in general, but particularly to those incorporating hydrogen that cannot be fully characterized using diffraction techniques.

Lipids in biocalcification: contrasts and similarities between intimal and medial vascular calcification and bone by NMR

Pathomechanisms underlying vascular calcification biogenesis are still incompletely understood. Biomineral from human atherosclerotic intimal plaques; human, equine, and bovine medial vascular calcifications; and human and equine bone was released from collagenous organic matrix by sodium hydroxide/sodium hypochlorite digestion. Solid-state (13)C NMR of intimal plaque mineral shows signals from cholesterol/cholesteryl esters and fatty acids. In contrast, in mineral from pure medial calcifications and bone mineral, fatty acid signals predominate. Refluxing (chloroform/methanol) intimal plaque calcifications removes the cholesterylic but not the fatty acyl signals. The lipid composition of this refluxed mineral now closely resembles that of the medial and bone mineral, which is unchanged by reflux. Thus, intimal and medial vascular calcifications and bone mineral have in common a pool of occluded mineral-entrained fatty acyl-rich lipids. This population of fatty acid may contain methyl-branched fatty acids, possibly representing lipoprotein particle remnants. Cell signaling and mechanistic parallels between physiological (orthotopic) and pathological (ectopic) calcification are also reflected thus in the NMR spectroscopic fingerprints of mineral-associated and mineral-entrained lipids. Additionally the atherosclerotic plaque mineral alone shows a significant independent pool of cholesterylic lipids. Colocalization of mineral and lipid may be coincidental, but it could also reflect an essential mechanistic component of biomineralization.

Characterization of the phosphatic mineral of the barnacle Ibla cumingi at atomic level by solid-state nuclear magnetic resonance: comparison with other phosphatic biominerals

Ibliform barnacles are among the few invertebrate animals harnessing calcium phosphate to construct hard tissue. The (31)P solid-state NMR (SSNMR) signal from the shell plates of Ibla cumingi (Iblidae) is broader than that of bone, and shifted by ca 1 ppm to low frequency. (1)H-(31)P heteronuclear correlation (HETCOR) experiments show a continuum of different phosphorus/phosphate atomic environments, close to hydrogen populations with resonance frequencies between ca 10 and 20 ppm. Associated (1)H and (31)P chemical shifts argue the coexistence of weakly (high (31)P frequency, low (1)H frequency) to more strongly (lower (31)P frequency, higher (1)H frequency) hydrogen-bonded hydrogen phosphate-like molecular/ionic species. There is no resolved signal from discrete OH(-) ions. (13)C SSNMR shows chitin, protein and other organic biomolecules but, unlike bone, there are no significant atomic scale organic matrix-mineral contacts. The poorly ordered hydrogen phosphate-like iblid mineral is strikingly different, structurally and compositionally, from both vertebrate bone mineral and the more crystalline fluoroapatite of the linguliform brachiopods. It probably represents a previously poorly characterized calcium phosphate biomineral, the evolution of which may have reflected either the chemical conditions of ancestral seas or the mechanical advantages of phosphatic biomineralization over a calcium carbonate equivalent.

Collagen atomic scale molecular disorder in ochronotic cartilage from an alkaptonuria patient, observed by solid state NMR

In pilot studies of the usefulness of solid state nuclear magnetic resonance spectroscopy in characterizing chemical and molecular structural effects of alkaptonuria on connective tissue, we have obtained (13) C spectra from articular cartilage from an AKU patient. An apparently normal anatomical location yielded a cross polarization magic angle spinning spectrum resembling literature spectra and dominated by collagen and glycosaminoglycan signals. All spectral linewidths from strongly pigmented ochronotic cartilage however were considerably increased relative to the control indicating a marked increase in collagen molecular disorder. This disordering of cartilage structural protein parallels, at the atomic level, the disordering revealed at higher length scales by microscopy. We also demonstrate that the abnormal spectra from ochronotic cartilage fit with the abnormality in the structure of collagen fibres at the ultrastructural level, whereby large ochronotic deposits appear to alter the structure of the collagen fibre by invasion and cross linking.

SUMMARY

Increased signal linewidths in solid state NMR spectra of ochronotic articular cartilage from an AKU patient relative to linewidths in normal, control, cartilage reveals a marked decrease in collagen molecular order in the diseased tissue. This atomic level disordering parallels higher length scale disorder revealed by microscopic techniques.

Apatite in kidney stones is a molecular composite with glycosaminoglycans and proteins: evidence from nuclear magnetic resonance spectroscopy, and relevance to Randall's plaque, pathogenesis and prophylaxis

PURPOSE

We characterized the biomacromolecular composition of phosphatic urinary stones using solid state nuclear magnetic resonance spectroscopy. We identified possible parallels between the nature of the organic matrix-mineral interface in stones and that in other mineralized tissue using nuclear magnetic resonance spectroscopy rotational echo double resonance.

MATERIALS AND METHODS

We analyzed 28 phosphatic (apatite and mixed apatite-struvite) surgically removed stones by nuclear magnetic resonance spectroscopy using (31)P, (13)C and a 9.4 Tesla magnetic field. Ten samples had sufficient signal from biomacromolecular organic material to characterize the mineral/organic interface by (13)C{(31)P} rotational echo double resonance.

RESULTS

Biomacromolecular organic material was most abundant in phosphatic stones in which apatite predominated. Nuclear magnetic resonance spectroscopy detected variable proportions of protein, glycosaminoglycan, lipid and carbonate. Rotational echo double resonance revealed strong interaction between mineral and glycosaminoglycan molecules, and to a lesser extent protein molecules, on the sub-nm length scale, implying that glycosaminoglycan and protein are composited into or onto the mineral lattice by strong physicochemical interactions. Carbonate ions substituted into apatite crystal lattices also showed the expected strong (13)C{(31)P} rotational echo double resonance effects. Conversely when present, lipid, calcium oxalate hydrates and uric acid showed no rotational echo double resonance effects, proving that they exist as deposits or crystals distinct from phosphatic mineral/biomacromolecular composites.

CONCLUSIONS

The intimate coexistence of biomacromolecules, especially glycosaminoglycan, with apatite in phosphatic stones supports the notion that they may have a key role in stone pathogenesis. The underlying intermolecular relationships may reflect those governing the formation of Randall's plaque in nascent stones.

Contrasts between organic participation in apatite biomineralization in brachiopod shell and vertebrate bone identified by nuclear magnetic resonance spectroscopy

Unusually for invertebrates, linguliform brachiopods employ calcium phosphate mineral in hard tissue formation, in common with the evolutionarily distant vertebrates. Using solid-state nuclear magnetic resonance spectroscopy (SSNMR) and X-ray powder diffraction, we compare the organic constitution, crystallinity and organic matrix-mineral interface of phosphatic brachiopod shells with those of vertebrate bone. In particular, the organic-mineral interfaces crucial for the stability and properties of biomineral were probed with SSNMR rotational echo double resonance (REDOR). Lingula anatina and Discinisca tenuis shell materials yield strikingly dissimilar SSNMR spectra, arguing for quite different organic constitutions. However, their fluoroapatite-like mineral is highly crystalline, unlike the poorly ordered hydroxyapatite of bone. Neither shell material shows (13)C{(31)P} REDOR effects, excluding strong physico-chemical interactions between mineral and organic matrix, unlike bone in which glycosaminoglycans and proteins are composited with mineral at sub-nanometre length scales. Differences between organic matrix of shell material from L. anatina and D. tenuis, and bone reflect evolutionary pressures from contrasting habitats and structural purposes. The absence of organic-mineral intermolecular associations in brachiopod shell argues that biomineralization follows different mechanistic pathways to bone; their details hold clues to the molecular structural evolution of phosphatic biominerals, and may provide insights into novel composite design.

Bisphosphonate protonation states, conformations, and dynamics on bone mineral probed by solid-state NMR without isotope enrichment

Recognition of bone mineral by bisphosphonates is crucial to their targeting, efficacy, therapeutic and diagnostic applications, and pharmacokinetics. In a search for rapid and simple NMR approaches to assessing the bone recognition characteristics of bisphosphonates, we have studied alendronate, pamidronate, neridronate, zoledronate and tiludronate, in crystalline form and bound to the surface of pure bone mineral stripped of its organic matrix by a simple chemical process. (31)P NMR chemical shift anisotropies and asymmetries in the crystalline compounds cluster strongly into groupings corresponding to fully protonated, monoprotonated, and deprotonated phosphonate states. All the mineral-bound bisphosphonates cluster in the same anisotropy-asymmetry space as the deprotonated phosphonates. In (13)C{(31)P} rotational echo double resonance (REDOR) experiments, which are sensitive to carbon-phosphorus interatomic distances, the strongly mineral-bound alendronate displays very similar conformational and side chain dynamics to its crystalline state. Pamidronate and neridronate, with shorter and longer sidechains, respectively, and generally weaker mineral binding, display more dynamical sidechains in the mineral-bound state. The REDOR experiment provides a simple rationalization of bisphosphonate-mineral affinity in terms of molecular structure and dynamics, consistent with findings from much more labour- and time-intensive isotope labelling approaches.

The mineral phase of calcified cartilage: its molecular structure and interface with the organic matrix

We have studied the atomic level structure of mineralized articular cartilage with heteronuclear solid-state NMR, our aims being to identify the inorganic species present at the surfaces of the mineral crystals which may interact with the surrounding organic matrix and to determine which components of the organic matrix are most closely involved with the mineral crystals. One-dimensional (1)H and (31)P and two-dimensional (1)H-(31)P heteronuclear correlation NMR experiments show that the mineral component is very similar to that in bone with regard to its surface structure. (13)C{(31)P} rotational echo double resonance experiments identify the organic molecules at the mineral surface as glycosaminoglycans, which concurs with our recent finding in bone. There is also evidence of gamma-carboxyglutamic acid residues interacting with the mineral. However, other matrix components appear more distant from the mineral compared with bone. This may be due to a larger hydration layer on the mineral crystal surfaces in calcified cartilage.

Correlating sideband patterns with powder patterns for accurate determination of chemical shift parameters in solid-state NMR

Powder patterns and sideband patterns have different strengths when it comes to using them to determine chemical shift parameters. Here, we show that chemical shift parameters can be determined with high accuracy by analysing the correlation pattern from a 2D experiment which correlates a powder pattern in the indirect dimension with a sideband pattern in the direct dimension. The chemical shift parameters so determined have greater accuracy than those obtained by analysing a sideband or powder pattern alone, for the same signal-to-noise ratio. This method can be applied for both resolved correlation patterns and to cases where two components share similar isotropic chemical shifts. The methodology is demonstrated in this paper, both theoretically and experimentally, on the (31)P signals of the bis-phosphonate drug, pamidronate.

Mineral surface in calcified plaque is like that of bone: further evidence for regulated mineralization

OBJECTIVE

Cell biological studies demonstrate remarkable similarities between mineralization processes in bone and vasculature, but knowledge of the components acting to initiate mineralization in atherosclerosis is limited. The molecular level microenvironment at the organic-inorganic interface holds a record of the mechanisms controlling mineral nucleation. This study was undertaken to compare the poorly understood interface in mineralized plaque with that of bone, which is considerably better characterized.

METHODS AND RESULTS

Solid state nuclear magnetic resonance (SSNMR) spectroscopy provides powerful tools for studying the organic-inorganic interface in calcium phosphate biominerals. The rotational echo double resonance (REDOR) technique, applied to calcified human plaque, shows that this interface predominantly comprises sugars, most likely glycosaminoglycans (GAGs). In this respect, and in the pattern of secondary effects seen to protein (mainly collagen), calcified plaque strongly resembles bone.

CONCLUSIONS

The similarity between biomineral formed under highly controlled (bone) and pathological (plaque) conditions suggests that the control mechanisms are more similar than previously thought, and may be adaptive. It is strong further evidence for regulation of plaque mineralization by osteo/chondrocytic vascular smooth muscle cells.

Towards a model of the mineral-organic interface in bone: NMR of the structure of synthetic glycosaminoglycan- and polyaspartate-calcium phosphate composites

We have synthesised three materials-chondroitin sulphate (ChS, a commercial product derived from shark cartilage and predominantly chondroitin-6-sulphate (Ch-6-S)) bound to pre-formed hydroxyapatite (HA, Ca(10)(PO(4))(6)(OH)(2)), HA formed in the presence of ChS and poly-Asp bound to pre-formed HA-to generate models for the mineral-organic interface in bone. The three materials have been investigated by (13)C cross polarisation magic-angle spinning (CPMAS) NMR, (13)C{(31)P} rotational echo double resonance (REDOR) and powder x-ray diffraction (XRD) in order to verify their composition and to determine the nature of their binding to HA. Our results show that for HA formed in the presence of Ch-6-S, all carbon atoms in the Ch-6-S having contact with mineral phosphate. We propose that HA in this case forms all around the Ch-6-S polymer rather than along one face of it as is more commonly supposed in cases of templating by organic molecules. However, Ch-6-S binding to pre-formed HA probably occurs via a surface layer of water on the mineral rather than to the mineral directly. In contrast, poly-Asp binds closely to the pre-formed HA surface and so is clearly able to displace at least some of the surface-bound water.

Exploring the relationship between cocrystal stability and symmetry: is Wallach's rule applicable to multi-component solids?

Comparison of structure and hydration stability of pairs of chiral and racemic binary cocrystals indicates that the racemic solid is more stable than the chiral one; we illustrate that this difference might arise from intermolecular (crystal packing) factors in one case, while intramolecular (molecular conformation) factors are more significant in the other.

Using chemical shift anisotropy to resolve isotropic signals in solid-state NMR

A key problem in solid-state NMR is resolving overlapping isotropic signals. We present here a two-dimensional method which can enable sites with the same isotropic chemical shift to be distinguished according to their chemical shift anisotropy and asymmetry. The method involves correlating sideband spectra at different effective spinning rates using CSA-amplification pulse sequences. The resulting two-dimensional correlation pattern allows very accurate determination of the chemical shift principal values in addition to the recovery of parameters for two overlapping patterns which allows the resolution of overlapping signals.

Enforcing Ostwald's rule of stages: Isolation of paracetamol forms III and II

We have been able to isolate and study the polymorphic form III of paracetamol using a specially designed methodology. Our work represents the first report of a reproducible, reliable route to form III. This has been an outstanding problem for over quarter of a century. Our method may be applicable to the isolation of metastable polymorphs of other compounds.

Structural, Solid-State NMR and Theoretical Studies of the Inverse-Coordination of Lithium Chloride Using Group 13 Phosphide Hosts

The reaction of MeAlCl2 with 'PhPLi2' in THF gives [{MeAl(PPh)3Li(4).3 THF}4(mu4-Cl)]-Li+ (1). The GaIII and InIII analogues, [{MeE(PPh)3Li(4).3 THF}4(mu4-Cl)]-Li+(THF)3 (E=Ga (2), In (3)), are obtained by the in situ reactions of MeECl2 with PhPLi2 in THF. For all of the complexes, the cage anions have an unusual cubic arrangement that is similar to a zeolite, and contain large voids (ca. 17 A). The location of the Li+ counterions in 1-3 and their coordination environment appears to subtly reflect variations in packing and lattice energy. Whereas in 1 highly mobile, loosely coordinated Li+ counterions are present, 2 and 3 contain less mobile THF-solvated counterions within the cavities. X-ray crystallographic and solid-state NMR studies are reported on 1-3, together with model DFT calculations on the selectivity of halide coordination.

Decoupling residual dipolar coupling between 13C and14N spin pairs in CPMAS NMR

Decoupling of the residual dipolar coupling between (13)C and(14)N nuclei is investigated experimentally in a triple resonance experiment. It is shown that pulsed decoupling can be used to give enhanced sensitivity and reduced line widths and the technique is illustrated using short peptides.

Ossicular density in golden moles (Chrysochloridae)

The densities of middle ear ossicles of golden moles (family Chrysochloridae, order Afrosoricida) were measured using the buoyancy method. The internal structure of the malleus was examined by high-resolution computed tomography, and solid-state NMR was used to determine relative phosphorus content. The malleus density of the desert golden mole Eremitalpa granti (2.44 g/cm3) was found to be higher than that reported in the literature for any other terrestrial mammal, whereas the ossicles of other golden mole species are not unusually dense. The increased density in Eremitalpa mallei is apparently related both to a relative paucity of internal vascularization and to a high level of mineralization. This high density is expected to augment inertial bone conduction, used for the detection of seismic vibrations, while limiting the skull modifications needed to accommodate the disproportionately large malleus. The mallei of the two subspecies of E. granti, E. g. granti and E. g. namibensis, were found to differ considerably from one another in both size and shape.

Recoupling of chemical-shift anisotropy powder patterns in MAS NMR

A comparison of three different implementations of the chemical-shift recoupling experiment of Tycko et al. [R. Tycko, G. Dabbagh, P.A. Mirau, Determination of chemical-shift-anisotropy lineshapes in a two-dimensional magic-angle-spinning NMR experiment, J. Magn. Reson. 85 (1989) 265-274] is presented. The methods seek to reduce the effects of artefacts resulting from pulse imperfections and residual C-H dipolar coupling in organic solids. An optimised and constant time implementation are shown to give well-defined and artefact free powder pattern lineshapes in the indirectly observed dimension for both sp2 and sp3 carbon sites. Experimental setup is no more demanding than for the original experiment, and can be implemented using standard commercial hardware.

Applications of the CSA-amplified PASS experiment

The recently reported CSA-amplified PASS experiment correlates the spinning sidebands at the true spinning frequency omega(r) with the spinning sidebands that would be obtained at the effective spinning frequency omega(r)/N, where N is termed the scaling factor. The experiment is useful for the measurement of small chemical shift anisotropies, for which slow magic-angle spinning frequencies, required to measure several spinning sidebands, can be unstable. We have experimentally evaluated the reliability of this experiment for this application. In particular we have demonstrated that large scaling factors of the order of N=27 may be used, whilst still obtaining accurate chemical shift sideband intensities at the effective spinning frequency from the F(1) projection. Moreover, the sideband intensities are accurately obtained even in the presence of significant pulse imperfections. A second application of the CSA-amplified PASS experiment is the measurement of the chemical shift anisotropy of sites that experience homonuclear dipolar coupling, as may be found in uniformly labelled biological molecules, or for nuclei with a high natural abundance. The effects of homonuclear dipolar coupling on CSA-amplified PASS spectra has been investigated by numerical simulations and are demonstrated using uniformly (13)C enriched l-histidine monohydrochloride monohydrate.