Solid-state NMR studies of collagen-based parchments and gelatin

Cyanophycin modifications for applications in tissue scaffolding

Cyanophycin (CGP) is a polypeptide consisting of amino acids-aspartic acid in the backbone and arginine in the side chain. Owing to its resemblance to cell adhesive motifs in the body, it can be considered suitable for use in biomedical applications as a novel component to facilitate cell attachment and tissue regeneration. Although it has vast potential applications, starting with nutrition, through drug delivery and tissue engineering to the production of value-added chemicals and biomaterials, CGP has not been brought to the industry yet. To develop scaffolds using CGP powder produced by bacteria, its properties (e.g., biocompatibility, morphology, biodegradability, and mechanical strength) should be tailored in terms of the requirements of the targeted tissue. Crosslinking commonly stands for a primary modification method for renovating biomaterial features to these extents. Herein, we aimed to crosslink CGP for the first time and present a comparative study of different methods of CGP crosslinking including chemical, physical, and enzymatic methods by utilizing glutaraldehyde (GTA), UV exposure, genipin, 1-ethyl-3-[3-dimethylaminopropyl] carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS), and monoamine oxidase (MAO). Crosslinking efficacy varied among the samples crosslinked via the different crosslinking methods. All crosslinked CGP were non-cytotoxic to L929 cells, except for the groups with higher GTA concentrations. We conclude that CGP is a promising candidate for scaffolding purposes to be used as part of a composite with other biomaterials to maintain the integrity of scaffolds. The initiative study demonstrated the unknown characteristics of crosslinked CGP, even though its feasibility for biomedical applications should be confirmed by further examinations. KEY POINTS: • Cyanophycin was crosslinked by 5 different methods • Crosslinked cyanophycin is non-cytotoxic to L929 cells • Crosslinked cyanophycin is a promising new material for scaffolding purposes.

Waste to Wealth Approach: Improved Antimicrobial Properties in Bioactive Hydrogels through Humic Substance-Gelatin Chemical Conjugation

Exploring opportunities for biowaste valorization, herein, humic substances (HS) were combined with gelatin, a hydrophilic biocompatible and bioavailable polymer, to obtain 3D hydrogels. Hybrid gels (Gel HS) were prepared at different HS contents, exploiting physical or chemical cross-linking, through 1-ethyl-(3-3-dimethylaminopropyl)carbodiimide (EDC) chemistry, between HS and gelatin. Physicochemical features were assessed through rheological measurements, X-ray diffraction, attenuated total reflectance (ATR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and scanning electron microscopy (SEM). ATR and NMR spectroscopies suggested the formation of an amide bond between HS and Gel via EDC chemistry. In addition, antioxidant and antimicrobial features toward both Gram(-) and Gram(+) strains were evaluated. HS confers great antioxidant and widespread antibiotic performance to the whole gel. Furthermore, the chemical cross-linking affects the viscoelastic behavior, crystalline structures, water uptake, and functional performance and produces a marked improvement of biocide action.

Unraveling the Complex Solid-State Phase Transition Behavior of 1-Iodoadamantane, a Material for Which Ostensibly Identical Crystals Undergo Different Transformation Pathways

Phase transitions in crystalline molecular solids have important implications in the fundamental understanding of materials properties and in the development of materials applications. Herein, we report the solid-state phase transition behavior of 1-iodoadamantane (1-IA) investigated using a multi-technique strategy [synchrotron powder X-ray diffraction (XRD), single-crystal XRD, solid-state NMR, and differential scanning calorimetry (DSC)], which reveals complex phase transition behavior on cooling from ambient temperature to ca. 123 K and on subsequent heating to the melting temperature (348 K). Starting from the known phase of 1-IA at ambient temperature (phase A), three low-temperature phases are identified (phases B, C, and D); the crystal structures of phases B and C are reported, together with a re-determination of the structure of phase A. Remarkably, single-crystal XRD shows that some individual crystals of phase A transform to phase B, while other crystals of phase A transform instead to phase C. Results (from powder XRD and DSC) on cooling a powder sample of phase A are fully consistent with this behavior while also revealing an additional transformation pathway from phase A to phase D. Thus, on cooling, a powder sample of phase A transforms partially to phase C (at 229 K), partially to phase D (at 226 K) and partially to phase B (at 211 K). During the cooling process, each of the phases B, C, and D is formed directly from phase A, and no transformations are observed between phases B, C, and D. On heating the resulting triphasic powder sample of phases B, C, and D from 123 K, phase B transforms to phase D (at 211 K), followed by the transformation of phase D to phase C (at 255 K), and finally, phase C transforms to phase A (at 284 K). From these observations, it is apparent that different crystals of phase A, which are ostensibly identical at the level of information revealed by XRD, must actually differ in other aspects that significantly influence their low-temperature phase transition pathways. This unusual behavior will stimulate future studies to gain deeper insights into the specific properties that control the phase transition pathways in individual crystals of this material.

Application of artificial neural networks to predict Young's moduli of cartilage scaffolds: An in-vitro and micromechanical study

In this study, four-phase Gelatin-Polypyrrole-Akermanite-Magnetite scaffolds were fabricated and analyzed using in-vitro tests and numerical simulations. Such scaffolds contained various amounts of Magnetite bioceramics as much as 0, 5, 10, and 15 wt% of Gelatin-Polypyrrole-Akermanite biocomposite. X-ray diffraction analysis and Fourier transform infrared spectroscopy were conducted. Swelling and degradation of the scaffolds were studied by immersing them in phosphate-buffered saline, PBS, solution. Magnetite bioceramics decreased the swelling percent and degradation duration. By immersing scaffolds in simulated body fluid, the highest formation rate of Apatite was observed in the 15 wt% Magnetite samples. The mean pore size was in an acceptable range to provide suitable conditions for cell proliferation. MG-63 cells were cultured on extracts of the scaffolds for 24, 48, and 72 h and their surfaces for 24 h. Cell viabilities and cell morphologies were assessed. Afterward, micromechanical models with spherical and polyhedral voids and artificial neural networks were employed to predict Young's moduli of the scaffolds. Based on the results of finite element analyses, spherical-shaped void models made the best predictions of elastic behavior in the 0, 5 wt% Magnetite scaffolds compared to the experimental data. Results of the simulations and experimental tests for the ten wt% Magnetite samples were well matched in both micromechanical models. In the 15 wt% Magnetite sample, models with polyhedral voids could precisely predict Young's modulus of such scaffolds.

Technical Note: Post-burial alteration of bones: Quantitative characterization with solid-state 1H MAS NMR

The identification of markers of the modifications occurring in human bones after death and of the sedimentary and post-sedimentary processes affecting their state of preservation, is of interest for several scientific disciplines. A new index, obtained from spectral deconvolution of the 1H MAS NMR spectra of bones, relating the number of organic protons to the amount of hydrogen nuclei in the OH- groups of bioapatite, is proposed as indicator of the state of preservation of the organic fraction. In the osteological material from three different archaeological sites, this index resulted positively correlated with the extent of collagen loss derived from infrared spectroscopy. Its sensitivity to changes in the physical and chemical characteristics of bone allows to identify distinct diagenetic pathways specific to each site and to distinguish different trajectories within the same site.

13 C solid-state NMR complemented by ATR-FTIR and micro-DSC to study modern collagen-based material and historical leather

Ancient vegetable tanned leathers and parchments are very complex materials in which both different manufacturing and deterioration processes make their study and chemical characterisation difficult. In this research, solid-state nuclear magnetic resonance (NMR) spectroscopy was applied to identify different tannin families (condensed and hydrolysable) in historical leather objects such as bookbindings, wall upholsters, footwear and accessories, and military apparel. Furthermore, leather deterioration with special focus on collagen gelatinisation was investigated. A comparison with Fourier transform infrared (FTIR) spectroscopy and micro-differential scanning calorimetry (micro-DSC) was also performed to support the ¹³ C CP-MAS NMR findings and to point out the advantages and limitations of solid-state NMR in analysing historical and archaeological leathers. A wide database of NMR and FTIR spectra of commercial tannins compounds was also collected in order to characterise historical and archaeological leathers.

Role of catechin on collagen type I stability upon oxidation: a NMR approach

The study focuses on the understanding, at molecular level, the mechanism of interaction between protein and flavonoids. Collagen and catechin interactions were investigated by NMR in solution and solid state. The effect of catechin on the stability of collagen to oxidation was also explored. Collagen was treated with two concentrations of catechin solutions. Oxidation was carried out by incubation of collagen solution with three oxidation systems: Fe(II)/H₂O₂, Cu(II)/H₂O₂, and NaOCl/H₂O₂. The effects of oxidation systems were evaluated by high resolution 1 D and 2 D proton spectroscopy and solid state NMR (¹³C CP MAS) experiments. Interactions between collagen and catechin preferentially occur between catechin B ring and the amino acids Pro and Hyp of collagen. Results showed that both iron and copper oxidation systems were able to interact with collagen by site specific attack. Moreover, catechin protects collagen proline from oxidation by metal/H₂O₂ systems, preventing copper and iron approach to collagene molecule;this behaviour was more evident for the copper/H₂O₂ system.

Biomacromolecules within bivalve shells: Is chitin abundant?

Bivalve shells are inorganic-organic nanocomposites whose material properties outperform their purely inorganic mineral counterparts. Most typically the inorganic phase is a polymorph of CaCO₃, while the organic phase contains biopolymers which have been presumed to be chitin and/or proteins. Identifying the biopolymer phase is therefore a crucial step in improving our understanding of design principles relevant to biominerals. In this work we study seven shells; four are examples of nacroprismatic shells (Alathyria jacksoni, Pinctada maxima, Hyriopsis cumingii and Cucumerunio novaehollandiae), one homogeneous (Arctica islandica), and two are crossed lamellar (Callista kingii, Tridacna gigas). Both intact shells, their organic extracts as isolated after decalcification in acid, and the periostracum overlay have been studied by solid-state CP-MAS NMR, FTIR, SEM and chemical analysis. In none of the shells examined in this work do we find a significant contribution to the organic fraction from chitin or its derivatives despite popular models of bivalve biomineralization which assume abundant chitin in the organic fraction of mollusk bivalve shells. In each of the nacroprismatic extracts the ¹³C NMR spectra represent similar proteinaceous material, Ala and Gly-rich and primarily organized as β-sheets. A different, yet highly conserved protein was found in the periostracum covering each of the three nacreous shells studied. The Arctica islandica shells with homogeneous microstructure contained proteins which do not appear to be silk-like, while in the crossed lamellar shells we extracted too little organic matter to characterize. STATEMENT OF SIGNIFICANCE: Hydrophobic macromolecules are structural components within the calcareous inorganic matrix of bivalve shells and are responsible for enhanced materials properties of the biominerals. Prevalent models suggest that chitin is such major hydrophobic component. Contrary to that we show that chitin is rare within the hydrophobic biopolymers which primarily consist of proteinaceous matter with structural motifs as silk-like β-sheets, or others yet to be determined. Recognizing that diverse proteinaceous motifs, devoid of abundant chitin, can yield the optimized mechanical properties of bivalve shells is critical both to understand the mechanistic pathways by which they regulate biomineralization and for the design of novel bioinspired materials.

Tin chemical shift anisotropy in tin dioxide: On ambiguity of CSA asymmetry derived from MAS spectra

Two different axial symmetries of the ¹¹⁹Sn chemical shift anisotropy (CSA) in tin dioxide with the asymmetry parameter (η) of 0 and 0.27 were reported previously based on the analysis of MAS NMR spectra. By analyzing the static powder pattern, we show that the ¹¹⁹Sn CSA is axially symmetric. A nearly axial symmetry and the principal axis system of the ¹¹⁹Sn chemical shift tensor in SnO₂ were deduced from periodic scalar-relativistic density functional theory (DFT) calculations of NMR parameters. The implications of fast small-angle motions on CSA parameters were also considered, which could potentially lead to a CSA symmetry in disagreement with a crystal symmetry. Our analysis of experimental spectra using spectral simulations and iterative fittings showed that MAS spectra recorded at relatively high frequencies do not show sufficiently distinct features in order to distinguish CSAs with η ≈ 0 and η ≈ 0.4. The example of SnO₂ shows that both the MAS lineshape and spinning sideband analyses may overestimate the η value by as much as ∼0.3 and ∼0.4, respectively. The results confirm that a static powder pattern must be analysed in order to improve the accuracy of the CSA asymmetry measurements. The measurements on SnO₂ nanoparticles showed that the asymmetry parameter of the ¹¹⁹Sn CSA increases for nm-sized particles with a larger surface area compared to μm-sized particles. The increase of the η value for tin atoms near the surface in SnO₂ was also confirmed by DFT calculations.

Pregnancy-Induced Dynamical and Structural Changes of Reproductive Tract Collagen

The tissues and organs of the female reproductive tract and pelvic floor undergo significant remodeling and alterations to allow for fetal growth and birth. In this work, we report on a study of the alterations of murine reproductive tract collagen resulting from pregnancy and parturition by spectrophotometry, histology, and (13)C, (2)H nuclear magnetic resonance (NMR). Four different cohorts of rats were investigated that included virgin, multiparous, two- and fourteen-day postpartum primiparous rats. (13)C CPMAS NMR revealed small chemical shift differences across the cohorts. The measured H-C internuclear correlation times indicated differences in dynamics of some motifs. However, the dynamics of the major amino acids, e.g., Gly, remained unaltered with respect to parity. (2)H NMR relaxation measurements revealed an additional water reservoir in the postpartum and multiparous cohorts pointing to redistribution of water due to pregnancy and/or parturition. Spectrophotometric measurements indicated that the collagen content in virgin rats was highest. Histological analysis of the upper vaginal wall indicated a signature of collagen fiber dissociation with smooth muscle and a change in the density of collagen fibers in multiparous rats.

1 H NMR study and multivariate data analysis of reindeer skin tanning methods

Reindeer skin clothing has been an essential component in the lives of indigenous people of the arctic and sub-arctic regions, keeping them warm during harsh winters. However, the skin processing technology, which often conveys the history and tradition of the indigenous group, has not been well documented. In this study, NMR spectra and relaxation behaviors of reindeer skin samples treated with a variety of vegetable tannin extracts, oils and fatty substances are studied and compared. With the assistance of principal component analysis (PCA), one can recognize patterns and identify groupings of differently treated samples. These methods could be important aids in efforts to conserve museum leather artifacts with unknown treatment methods and in the analysis of reindeer skin tanning processes. Copyright © 2016 John Wiley & Sons, Ltd.

Selective detection and complete identification of triglycerides in cortical bone by high-resolution (1)H MAS NMR spectroscopy

Using (1)H-based magic angle spinning solid-state NMR spectroscopy, we report an atomistic-level characterization of triglycerides in compact cortical bone. By suppressing contributions from immobile molecules present in bone, we show that a (1)H-based constant-time uniform-sign cross-peak (CTUC) two-dimensional COSY-type experiment that correlates the chemical shifts of protons can selectively detect a mobile triglyceride layer as the main component of small lipid droplets embedded on the surface of collagen fibrils. High sensitivity and resolution afforded by this NMR approach could be potentially utilized to investigate the origin of triglycerides and their pathological roles associated with bone fractures, diseases, and aging.

Can ultrashort-TE (UTE) MRI sequences on a 3-T clinical scanner detect signal directly from collagen protons: freeze-dry and D2 O exchange studies of cortical bone and Achilles tendon specimens

Ultrashort-TE (UTE) sequences can obtain signal directly from short-T2 , collagen-rich tissues. It is generally accepted that bound and free water can be detected with UTE techniques, but the ability to detect protons directly on the collagen molecule remains controversial. In this study, we investigated the potential of UTE sequences on a 3-T clinical scanner to detect collagen protons via freeze-drying and D2 O-H2 O exchange studies. Experiments were performed on bovine cortical bone and human Achilles tendon specimens, which were either subject to freeze-drying for over 66 h or D2 O-H2 O exchange for 6 days. Specimens were imaged using two- and three-dimensional UTE with Cones trajectory techniques with a minimum TE of 8 μs at 3 T. UTE images before treatment showed high signal from all specimens with bi-component T2 * behavior. Bovine cortical bone showed a shorter T2 * component of 0.36 ms and a longer T2 * component of 2.30 ms with fractions of 78.2% and 21.8% by volume, respectively. Achilles tendon showed a shorter T2 * component of 1.22 ms and a longer T2 * component of 15.1 ms with fractions of 81.1% and 18.9% by volume, respectively. Imaging after freeze-drying or D2 O-H2 O exchange resulted in either the absence or near-absence of signal. These results indicate that bound and free water are the sole sources of UTE signal in bovine cortical bone and human Achilles tendon samples on a clinical 3-T scanner. Protons on the native collagen molecule are not directly visible when imaged using UTE sequences. Copyright © 2016 John Wiley & Sons, Ltd.

Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR

Solid-state NMR studies of collagen samples of various origins confirm that the amplitude of collagen backbone and sidechain motions increases significantly on increasing the water content. This conclusion is supported by the changes observed in three different NMR observables: (i) the linewidth dependence on the 1H decoupling frequency; (ii) 13C CSA changes for the peptide carbonyl groups, and (iii) dephasing rates of 1H-13C dipolar couplings. In particular, a nearly threefold increase in motional amplitudes of the backbone librations about C-Cα or N-Cα bonds was found on increasing the added water content up to 47 wt%D2 O. On the basis of the frequencies of NMR observables involved, the timescale of the protein motions dependent on the added water content is estimated to be of the order of microseconds. This estimate agrees with that from wideline T2(1)H NMR measurements. Also, our wideline 1H NMR measurements revealed that the timescale of the microsecond motions in proteins reduces significantly on increasing the added water content, i.e., an ∼15-fold increase in protein motional frequencies is observed on increasing the added water content to 45 wt% D2 O. The observed changes in collagen dynamics is attributed to the increase in water translational diffusion on increasing the amount of added water, which leads to more frequent "bound water/free water" exchange on the protein surface, accompanied by the breakage and formation of new hydrogen bonds with polar functionalities of protein.

Ultra fast magic angle spinning solid - state NMR spectroscopy of intact bone

Ultra fast magic angle spinning (MAS) has been a potent method to significantly average out homogeneous/inhomogeneous line broadening in solid-state nuclear magnetic resonance (ssNMR) spectroscopy. It has given a new direction to ssNMR spectroscopy with its different applications. We present here the first and foremost application of ultra fast MAS (~60 kHz) for ssNMR spectroscopy of intact bone. This methodology helps to comprehend and elucidate the organic content in the intact bone matrix with resolution and sensitivity enhancement. At this MAS speed, amino protons from organic part of intact bone start to appear in (1) H NMR spectra. The experimental protocol of ultra-high speed MAS for intact bone has been entailed with an additional insight achieved at 60 kHz.

Predominant role of water in native collagen assembly inside the bone matrix

Bone is one of the most intriguing biomaterials found in nature consisting of bundles of collagen helixes, hydroxyapatite, and water, forming an exceptionally tough, yet lightweight material. We present here an experimental tool to map water-dependent subtle changes in triple helical assembly of collagen protein in its absolute native environment. Collagen being the most abundant animal protein has been subject of several structural studies in last few decades, mostly on an extracted, overexpressed, and synthesized form of collagen protein. Our method is based on a (1)H detected solid-state nuclear magnetic resonance (ssNMR) experiment performed on native collagen protein inside intact bone matrix. Recent development in (1)H homonuclear decoupling sequences has made it possible to observe specific atomic resolution in a large complex system. The method consists of observing a natural-abundance two-dimensional (2D) (1)H/(13)C heteronuclear correlation (HETCOR) and(1)H double quantum-single quantum (DQ-SQ) correlation ssNMR experiment. The 2D NMR experiment maps three-dimensional assembly of native collagen protein and shows that extracted form of collagen protein is significantly different from protein in the native state. The method also captures native collagen subtle changes (of the order of ∼1.0 Å) due to dehydration and H/D exchange, giving an experimental tool to map small changes. The method has the potential to be of wide applicability to other collagen containing biomaterials.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

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.

NMR investigation of the role of osteocalcin and osteopontin at the organic-inorganic interface in bone

Mechanical resilience of bone tissue decreases with age. The ability to comprehensively probe and understand bone properties could help alleviate this problem. One important aspect of bone quality that has recently been made evident is the presence of dilatational bands formed by osteocalcin (OC) and osteopontin (OPN), which contribute to fracture toughness. However, experimental evidence of the structural role of these two proteins at the organic-mineral interface in bone is still needed. Solid state nuclear magnetic resonance (SSNMR) is emerging as a useful technique in probing molecular level aspects of bone. Here, we present the first SSNMR study of bone tissue from genetically modified mice lacking OC and/or OPN. Probing the mineral phase, the organic matrix and their interface revealed that, despite the absence of OC and OPN, the organic matrix and mineral were well preserved, and the overall exposure of collagen to hydroxyapatite (HA) nanoparticles was hardly affected. However, the proximity to the HA surface was slightly increased for a number of bone components including less abundant amino acids like lysine, suggesting that this is how the tissue compensates for the lack of OC and OPN. Taken together, the NMR data supports the recently proposed model, in which the contribution of OC-OPN to fracture toughness is related to their presence at the extrafibrillar organic-mineral interfaces, where they reinforce the network of mineralized fibrils and form dilatational bands. In an effort toward further understanding the structural role of individual amino acids of low abundance in bone, we then explored the possibility of specific (13)C enrichment of mouse bone, and report the first SSNMR spectra of 97% (13)C lysine-enriched tissue. Results show that such isotopic enrichment allows valuable molecular-level structural information to be extracted, and sheds light on post-translational modifications undergone by specific amino acids in vivo.

Crystallinity and compositional changes in carbonated apatites: Evidence from 31P solid-state NMR, Raman, and AFM analysis

Solid-state (magic-angle spinning) NMR spectroscopy is a useful tool for obtaining structural information on bone organic and mineral components and synthetic model minerals at the atomic-level. Raman and 31P NMR spectral parameters were investigated in a series of synthetic B-type carbonated apatites (CAps). Inverse 31P NMR linewidth and inverse Raman PO43- ν1 bandwidth were both correlated with powder XRD c-axis crystallinity over the 0.3-10.3 wt% CO32- range investigated. Comparison with bone powder crystallinities showed agreement with values predicted by NMR and Raman calibration curves. Carbonate content was divided into two domains by the 31P NMR chemical shift frequency and the Raman phosphate ν1 band position. These parameters remain stable except for an abrupt transition at 6.5 wt% carbonate, a composition which corresponds to an average of one carbonate per unit cell. This near-binary distribution of spectroscopic properties was also found in AFM-measured particle sizes and Ca/P molar ratios by elemental analysis. We propose that this transition differentiates between two charge-balancing ion-loss mechanisms as measured by Ca/P ratios. These results define a criterion for spectroscopic characterization of B-type carbonate substitution in apatitic minerals.

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use ¹³C NMR spin-lattice relaxation times T₁ of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc.

Concise NMR approach for molecular dynamics characterizations in organic solids

Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the α and γ polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics.

Solid-state NMR study reveals collagen I structural modifications of amino acid side chains upon fibrillogenesis

In vivo, collagen I, the major structural protein in human body, is found assembled into fibrils. In the present work, we study a high concentrated collagen sample in its soluble, fibrillar, and denatured states using one and two dimensional {(1)H}-(13)C solid-state NMR spectroscopy. We interpret (13)C chemical shift variations in terms of dihedral angle conformation changes. Our data show that fibrillogenesis increases the side chain and backbone structural complexity. Nevertheless, only three to five rotameric equilibria are found for each amino acid residue, indicating a relatively low structural heterogeneity of collagen upon fibrillogenesis. Using side chain statistical data, we calculate equilibrium constants for a great number of amino acid residues. Moreover, based on a (13)C quantitative spectrum, we estimate the percentage of residues implicated in each equilibrium. Our data indicate that fibril formation greatly affects hydroxyproline and proline prolyl pucker ring conformation. Finally, we discuss the implication of these structural data and propose a model in which the attractive force of fibrillogenesis comes from a structural reorganization of 10 to 15% of the amino acids. These results allow us to further understand the self-assembling process and fibrillar structure of collagen.

Concentration and Humidity Effect on Gelatin Films Studied by NMR

Gelatin films were prepared using different initial concentrations (1 to 30%) in H2O (w/v). The solid films were kept at four different environmental conditions at 20%, 43%, 75%, and 90% relative humidity, until complete equilibrium was achieved. Spin–spin relaxation (T 2) and spin–lattice relaxation (T 1) times of the samples were determined using a low-field nuclear magnetic resonance (NMR) spectrometer operated at 40 MHz proton (1H) Larmor frequency and were correlated with the molecular mobility of the system influenced by the humidity conditions and initial concentration. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) were performed as well to investigate the thermal properties of the samples. The results indicate an increase in molecular mobility of the gelatin films with the increase of storage humidity independent of the initial concentration and suggest that the dynamic of the films depends on the amount of the water in the amorphous region of the film.

High-resolution structural insights into bone: a solid-state NMR relaxation study utilizing paramagnetic doping

The hierarchical heterogeneous architecture of bone imposes significant challenges to structural and dynamic studies conducted by traditional biophysical techniques. High-resolution solid-state nuclear magnetic resonance (SSNMR) spectroscopy is capable of providing detailed atomic-level structural insights into such traditionally challenging materials. However, the relatively long data-collection time necessary to achieve a reliable signal-to-noise ratio (S/N) remains a major limitation for the widespread application of SSNMR on bone and related biomaterials. In this study, we attempt to overcome this limitation by employing the paramagnetic relaxation properties of copper(II) ions to shorten the (1)H intrinsic spin-lattice (T(1)) relaxation times measured in natural-abundance (13)C cross-polarization (CP) magic-angle-spinning (MAS) NMR experiments on bone tissues for the purpose of accelerating the data acquisition time in SSNMR. To this end, high-resolution solid-state (13)C CPMAS experiments were conducted on type I collagen (bovine tendon), bovine cortical bone, and demineralized bovine cortical bone, each in powdered form, to measure the (1)H T(1) values in the absence and in the presence of 30 mM Cu(II)(NH(4))(2)EDTA. Our results show that the (1)H T(1) values were successfully reduced by a factor of 2.2, 2.9, and 3.2 for bovine cortical bone, type I collagen, and demineralized bone, respectively, without reducing the spectral resolution and thus enabling faster data acquisition. In addition, paramagnetic quenching of particular (13)C NMR resonances on exposure to Cu(2+) ions in the absence of mineral was also observed, potentially suggesting the relative proximity of three main amino acids in the protein backbone (glycine, proline, and alanine) to the bone mineral surface.

Comprehensive multiphase NMR spectroscopy: basic experimental approaches to differentiate phases in heterogeneous samples

Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate (1)H and (13)C spectra for the different phases. In addition, (19)F performance is also addressed. To illustrate the capability of (19)F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state.

Solid state NMR investigation of intact human bone quality: balancing issues and insight into the structure at the organic-mineral interface

Age-related bone fragility fractures present a significant problem for public health. Measures of bone quality are increasingly recognized to complement the conventional bone mineral density (BMD) based assessment of fracture risk. The ability to probe and understand bone quality at the molecular level is desirable in order to unravel how the structure of organic matrix and its association with mineral contribute to the overall mechanical properties. The (13)C{(31)P} REDOR MAS NMR (Rotational Echo Double Resonance Magic Angle Spinning Nuclear Magnetic Resonance) technique is uniquely suited for the study of the structure of the organic-mineral interface in bone. For the first time, we have applied it successfully to analyze the structure of intact (non-powdered) human cortical bone samples, from young healthy and old osteoporotic donors. Loading problems associated with the rapid rotation of intact bone were solved using a Finite Element Analysis (FEA) approach, and a method allowing osteoporotic samples to be balanced and spun reproducibly is described. REDOR NMR parameters were set to allow insight into the arrangement of the amino acids at the mineral interface to be accessed, and SVD (Singular Value Decomposition) was applied to enhance the signal to noise ratio and enable a better analysis of the data. From the REDOR data, it was found that carbon atoms belonging to citrate/glucosaminoglycans (GAGs) are closest to the mineral surface regardless of age or site. In contrast, the arrangement of the collagen backbone at the interface varied with site and age. The relative proximity of two of the main amino acids in bone matrix proteins, hydroxyproline and alanine, with respect to the mineral phase was analyzed in more detail, and discussed in view of glycation measurements which were carried out on the tissues. Overall, this work shows that the (13)C{(31)P} REDOR NMR approach could be used as a complementary technique to assess a novel aspect of bone quality, the organic-mineral interface structure.

Improved MR-based characterization of engineered cartilage using multiexponential T2 relaxation and multivariate analysis

Noninvasive monitoring of tissue quality would be of substantial use in the development of cartilage tissue engineering strategies. Conventional MR parameters provide noninvasive measures of biophysical tissue properties and are sensitive to changes in matrix development, but do not clearly distinguish between groups with different levels of matrix development. Furthermore, MR outcomes are nonspecific, with particular changes in matrix components resulting in changes in multiple MR parameters. To address these limitations, we present two new approaches for the evaluation of tissue engineered constructs using MR, and apply them to immature and mature engineered cartilage after 1 and 5 weeks of development, respectively. First, we applied multiexponential T(2) analysis for the quantification of matrix macromolecule-associated water compartments. Second, we applied multivariate support vector machine analysis using multiple MR parameters to improve detection of degree of matrix development. Monoexponential T(2) values decreased with maturation, but without further specificity. Much more specific information was provided by multiexponential analysis. The T(2) distribution in both immature and mature constructs was qualitatively comparable to that of native cartilage. The analysis showed that proteoglycan-bound water increased significantly during maturation, from a fraction of 0.05 ± 0.01 to 0.07 ± 0.01. Classification of samples based on individual MR parameters, T(1), T(2), k(m) or apparent diffusion coefficient, showed that the best classifiers were T(1) and k(m), with classification accuracies of 85% and 84%, respectively. Support vector machine analysis improved the accuracy to 98% using the combination (k(m), apparent diffusion coefficient). These approaches were validated using biochemical and Fourier transform infrared imaging spectroscopic analyses, which showed increased proteoglycan and collagen with maturation. In summary, multiexponential T(2) and multivariate support vector machine analyses provide improved sensitivity to changes in matrix development and specificity to matrix composition in tissue engineered cartilage. These approaches show substantial potential for the evaluation of engineered cartilage tissue and for extension to other tissue engineering constructs.

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.

Improved specificity of cartilage matrix evaluation using multiexponential transverse relaxation analysis applied to pathomimetically degraded cartilage

The noninvasive early detection of specific matrix alterations in degenerative cartilage disease would be of substantial use in basic science studies and clinically, but remains an elusive goal. Recently developed MRI methods exhibit some specificity, but require contrast agents or nonstandard pulse sequences and hardware. We present a multiexponential approach which does not require contrast agents or specialized hardware, and uses a standard multiple-echo spin-echo sequence. Experiments were performed on tissue models of degenerative cartilage using enzymes with distinct actions. MR results were validated using histologic, biochemical and infrared spectroscopic analyses. The sulfated glycosaminoglycan per dry weight (dw) in bovine nasal cartilage was 0.72 ± 0.06 mg/mg dw and was reduced through chondroitinase AC and collagenase digestion to 0.56 ± 0.12 and 0.58 ± 0.13 mg/mg dw, respectively. Multiexponential analysis of data obtained at 9.4 T permitted the identification of tissue compartments assigned to the proteoglycan component of the matrix and to bulk water. Enzymatic treatment resulted in a significant reduction in the ratio of proteoglycan-bound to free water from 0.13 ± 0.02 in control cartilage to 0.03 ± 0.02 and 0.05 ± 0.06 under chondroitinase AC and collagenase treatment, respectively. As expected, monoexponential T(2) increased with both degradation protocols, but without further specificity to the nature of the degradation. An important eventual extension of this approach may be to map articular cartilage degeneration in the clinical setting. As an initial step towards this, localized multiexponential T(2) analysis was performed on control and trypsin treated excised bovine patella. The results obtained on this articular cartilage sample were readily interpretable in terms of proteoglycan-associated and relatively free water compartments. In potential clinical applications, signal-to-noise ratio constraints will define the threshold for the detection of macromolecular compartment changes at a given spatial scale. The multiexponential approach has potential application to the early detection of cartilage degradation with the use of appropriate pulse parameters under high signal-to-noise ratio conditions.

Mapping proteoglycan-bound water in cartilage: Improved specificity of matrix assessment using multiexponential transverse relaxation analysis

Association of MR parameters with cartilage matrix components remains an area of ongoing investigation. Multiexponential analysis of nonlocalized transverse relaxation data has previously been used to quantify water compartments associated with matrix macromolecules in cartilage. We extend this to mapping the proteoglycan (PG)-bound water fraction in cartilage, using mature and young bovine nasal cartilage model systems, toward the goal of matrix component-specific imaging. PG-bound water fraction from mature and young bovine nasal cartilage was 0.31 ± 0.04 and 0.22 ± 0.06, respectively, in agreement with biochemically derived PG content and PG-to-water weight ratios. Fourier transform infrared imaging spectroscopic-derived PG maps normalized by water content (IR-PG(ww) ) showed spatial correspondence with PG-bound water fraction maps. Extensive simulation analysis demonstrated that the accuracy and precision of our determination of PG-bound water fraction was within 2%, which is well-within the observed tissue differences. Our results demonstrate the feasibility of performing imaging-based multiexponential analysis of transverse relaxation data to map PG in cartilage.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources – mimosa, quebracho, chestnut and tara – are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 μs long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ϕ/ψ angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99ϕ, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: α(L) ⇆ β(PR) ⇆ β(S) ⇆ β(P) ⇆ α, where backbone secondary structures α(L) and α are associated with helices and turns, β(P) and β(PR) correspond to the left- and right-handed polyproline II structures and β(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals.

The effects of anticalcification treatments and hydration on the molecular dynamics of bovine pericardium collagen as revealed by 13C solid-state NMR

This article describes a solid-state NMR (SSNMR) investigation of the influence of hydration and chemical cross-linking on the molecular dynamics of the constituents of the bovine pericardium (BP) tissues and its relation to the mechanical properties of the tissue. Samples of natural phenethylamine-diepoxide (DE)- and glutaraldehyde (GL)-fixed BP were investigated by (13)C cross-polarization SSNMR to probe the dynamics of the collagen, and the results were correlated to the mechanical properties of the tissues, probed by dynamical mechanical analysis. For samples of natural BP, the NMR results show that the higher the hydration level the more pronounced the molecular dynamics of the collagen backbone and sidechains, decreasing the tissue's elastic modulus. In contrast, in DE- and GL-treated samples, the collagen molecules are more rigid, and the hydration seems to be less effective in increasing the collagen molecular dynamics and reducing the mechanical strength of the samples. This is mostly attributed to the presence of cross-links between the collagen plates, which renders the collagen mobility less dependent on the water absorption in chemically treated samples.

Time-resolved dehydration-induced structural changes in an intact bovine cortical bone revealed by solid-state NMR spectroscopy

Understanding the structure and structural changes of bone, a highly heterogeneous material with a complex hierarchical architecture, continues to be a significant challenge even for high-resolution solid-state NMR spectroscopy. While it is known that dehydration affects mechanical properties of bone by decreasing its strength and toughness, the underlying structural mechanism at the atomic level is unknown. Solid-state NMR spectroscopy, controlled dehydration, and H/D exchange were used for the first time to reveal the structural changes of an intact piece of bovine cortical bone. (1)H spectra were used to monitor the dehydration of the bone inside the rotor, and high-resolution (13)C chemical shift spectra obtained under magic-angle spinning were used evaluate the dehydration-induced conformational changes in the bone. The experiments revealed the slow denaturation of collagen due to dehydration while the trans-Xaa-Pro conformation in collagen remained unchanged. Our results suggest that glycosaminoglycans in the collagen fiber and mineral interface may chelate with a Ca(2+) ion present on the surface of the mineral through sulfate or carboxylate groups. These results provide insights into the role of water molecules in the bone structure and shed light on the relationship between the structure and mechanics of bone.

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.