31P and 13C solid-state NMR spectroscopy to study collagen synthesis and biomineralization in polymer-based bone implants

Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics

In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interactions inside the membrane serve to stabilize integral proteins, which span the lipid bilayer. This review investigates a number of computational and experimental methods used to study membrane proteins. It encompasses a variety of technologies, including electrophoresis, X-ray crystallography, cryogenic electron microscopy (cryo-EM), nuclear magnetic resonance spectroscopy (NMR), biophysical methods, computational methods, and artificial intelligence. The link between structure and function of membrane proteins has been better understood thanks to these approaches, which also hold great promise for future study in the field. The significance of fusing artificial intelligence with experimental data to improve our comprehension of membrane protein biology is also covered in this paper. This effort aims to shed light on the complexity of membrane protein biology by investigating a variety of experimental and computational methods. Overall, the goal of this review is to emphasize how crucial it is to understand the functions of membrane proteins in eukaryotic cells. It gives a general review of the numerous methods used to look into these crucial elements and highlights the demand for multidisciplinary approaches to advance our understanding.

Practical Aspects of NMR-Based Metabolomics

While NMR-based metabolomics is only about 20 years old, NMR has been a key part of metabolic and metabolism studies for >40 years. Historically, metabolic researchers used NMR because of its high level of reproducibility, superb instrument stability, facile sample preparation protocols, inherently quantitative character, non-destructive nature, and amenability to automation. In this chapter, we provide a short history of NMR-based metabolomics. We then provide a detailed description of some of the practical aspects of performing NMR-based metabolomics studies including sample preparation, pulse sequence selection, and spectral acquisition and processing. The two different approaches to metabolomics data analysis, targeted vs. untargeted, are briefly outlined. We also describe several software packages to help users process NMR spectra obtained via these two different approaches. We then give several examples of useful or interesting applications of NMR-based metabolomics, ranging from applications to drug toxicology, to identifying inborn errors of metabolism to analyzing the contents of biofluids from dairy cattle. Throughout this chapter, we will highlight the strengths and limitations of NMR-based metabolomics. Additionally, we will conclude with descriptions of recent advances in NMR hardware, methodology, and software and speculate about where NMR-based metabolomics is going in the next 5-10 years.

Scalable Synthesis of Hide Substance-Chitosan-Hydroxyapatite: Novel Biocomposite from Industrial Wastes and Its Efficiency in Dye Removal

A novel porous polymer-inorganic hybrid biocomposite with various functional groups (hide substance/chitosan/hydroxyapatite) has been synthesized in simple, economic, and scalable process utilizing leather industry solid waste and seafood industry waste composed with hydroxyapatite. Physicochemical characterization of the material reveals formation of composites with homogenous distribution of the constituents in the material matrix. The composite is hard and porous (with 0.1632 cm3/g slit-shaped mesopores and micropores) having particle sizes 40-80 μm and a Brunauer-Emmett-Teller surface area of 55.54 m2/g. The material is polycrystalline in nature with a fair amount of amorphous substance and less hydrophilic in character than constituent polymers. The dye removal efficiency of the material has been tested with two model dyes, namely, methylene blue (MB) (cationic/basic dye) and sunset yellow (SY) (anionic/acid dye). Optimum adsorptions of 3.8 mg MB (pH 12, RT ≈ 27 °C) and 168 mg of SY (pH 3, RT ≈ 27 °C) have been found per gram of the composite material. Langmuir isotherm and pseudo second order rate models have been found to be the best-fit models to explain the equilibrium isotherm and kinetics of the adsorption process for both the dyes. However, higher and faster adsorption of SY in comparison with MB indicated higher binding efficiency of the material toward the acidic dye. Desorption of dyes from the dye-adsorbed material was studied using a suitable eluent of appropriate pH and recycling for five times showed without loss of efficiency. The prepared composite showed very high dye removal efficiency toward four different commercially used dyes (496 mg/g of Orange-NR, 477 mg/g of Red-VLN, 488 mg/g of Blue-113 dye, and 274 mg/g of Green-PbS dye) from their individual and cocktail solutions. It was also efficient to decolorize dye-bearing tannery exhaust bath. Hence, waste materials generated during industrial processes could be efficiently used for the decontamination of colored wastewater produced by various industries.

NMR Techniques in Metabolomic Studies: A Quick Overview on Examples of Utilization

Metabolomics is a rapidly developing branch of science that concentrates on identifying biologically active molecules with potential biomarker properties. To define the best biomarkers for diseases, metabolomics uses both models (in vitro, animals) and human, as well as, various techniques such as mass spectroscopy, gas chromatography, liquid chromatography, infrared and UV-VIS spectroscopy and nuclear magnetic resonance. The last one takes advantage of the magnetic properties of certain nuclei, such as ¹H, ¹³C, ³¹P, ¹⁹F, especially their ability to absorb and emit energy, what is crucial for analyzing samples. Among many spectroscopic NMR techniques not only one-dimensional (1D) techniques are known, but for many years two-dimensional (2D, for example, COSY, DOSY, JRES, HETCORE, HMQS), three-dimensional (3D, DART-MS, HRMAS, HSQC, HMBC) and solid-state NMR have been used. In this paper, authors taking apart fundamental division of nuclear magnetic resonance techniques intend to shown their wide application in metabolomic studies, especially in identifying biomarkers.

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.

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.

New methods to study the composition and structure of the extracellular matrix in natural and bioengineered tissues

The extracellular matrix (ECM) comprises a gel of numerous biopolymers that occurs in a multitude of biological tissues. The ECM provides the basic support and mechanical strength of skeletal tissue and is responsible for shape retention. At the same time, the ECM is responsible for the viscoelastic properties and the elasticity of soft tissues. As expected, there are several important diseases that affect and degenerate the ECM with severe consequences for its properties. Bioengineering is a promising approach to support the regenerative capacity of the body. Unfortunately, the biomechanical properties of bioengineered ECM often only poorly meet the standards of their native counterparts. Many bioengineered tissues are characterized by an increased glycosaminoglycan (GAG) but decreased collagen content. This leads to an enhanced water content that strongly alters the viscoelastic and thus the biomechanical properties. Therefore, compositional analysis is important to estimate the tissue quality. We will show that nuclear magnetic resonance (NMR) spectroscopy and soft-ionization mass spectrometry (MS) represent useful techniques for ECM research both in natural and bioengineered tissues. Both methods are strongly complimentary: while MS techniques such as matrix-assisted laser desorption and ionization (MALDI) are excellent and very sensitive analytical tools to determine the collagen and the GAG contents of tissues, NMR spectroscopy provides insight into the molecular architecture of the ECM, its dynamics and other important parameters such as the water content of the tissue as well as the diffusion of molecules within the ECM.

Recent NMR developments applied to organic-inorganic materials

In this contribution, the latest developments in solid state NMR are presented in the field of organic-inorganic (O/I) materials (or hybrid materials). Such materials involve mineral and organic (including polymeric and biological) components, and can exhibit complex O/I interfaces. Hybrids are currently a major topic of research in nanoscience, and solid state NMR is obviously a pertinent spectroscopic tool of investigation. Its versatility allows the detailed description of the structure and texture of such complex materials. The article is divided in two main parts: in the first one, recent NMR methodological/instrumental developments are presented in connection with hybrid materials. In the second part, an exhaustive overview of the major classes of O/I materials and their NMR characterization is presented.

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.

Application of sodium triple-quantum coherence NMR spectroscopy for the study of growth dynamics in cartilage tissue engineering

We studied the tissue growth dynamics of tissue-engineered cartilage at an early growth stage after cell seeding for four weeks using sodium triple-quantum coherence NMR spectroscopy. The following tissue-engineering constructs were studied: 1) bovine chondrocytes cultured in alginate beads; 2) bovine chondrocytes cultured as pellets (scaffold-free chondrocyte pellets); and 3) human marrow stromal cells (HMSCs) seeded in collagen/chitosan based biomimetic scaffolds. We found that the sodium triple-quantum coherence spectroscopy could differentiate between different tissue-engineered constructs and native tissues based on the fast and slow components of relaxation rate as well as on the average quadrupolar coupling. Both fast (Tf ) and slow (Ts ) relaxation times were found to be longer in chondrocyte pellets and biomimetic scaffolds compared to chondrocytes suspended in alginate beads and human articular cartilage tissues. In all cases, it was found that relaxation rates and motion of sodium ions measured from correlation times were dependent on the amount of macromolecules, high cell density and anisotropy of the cartilage tissue-engineered constructs. Average quadrupolar couplings were found to be lower in the engineered tissue compared to native tissue, presumably due to the lack of order in collagen accumulated in the engineered tissue. These results support the use of sodium triple-quantum coherence spectroscopy as a tool to investigate anisotropy and growth dynamics of cartilage tissue-engineered constructs in a simple and reliable way.

On-resin synthesis of an acylated and fluorescence-labeled cyclic integrin ligand for modification of poly(lactic-co-glycolic acid)

Cyclic Arg-Gly-Asp (RGD) peptides show remarkable affinity and specificity to integrin receptors and mediate important physiological effects in tumor angiogenesis. Additionally, they are one of the keyplayers in improving the biocompatibility of biomaterials. The fully biodegradable polymer poly(lactic-co-glycolic acid) (PLGA) is frequently used for biomedical implants and can be applied as nanoparticles for drug delivery. The aim of this work was the generation of a lipidated c[RGDfK] peptide including a second functionality for coating of hydrophobic PLGA. Therefore, we established a general and straightforward strategy for the introduction of two different modifications into the same c[RGDfK] peptide. This allowed the generation of a palmitoylated integrin-binding lipopeptide that shows high affinity to PLGA. Additionally, we coupled 5(6)-carboxyfluorescein to the second site for modification to enable sensitive quantification of the immobilized lipopeptide on PLGA. In conclusion, we present a synthesis protocol that enables the preparation of c[RGDfK] lipopeptides with a strong affinity to PLGA and an additional site for modifications. This will provide the opportunity to introduce a variety of effector molecules site-specifically to the c[RGDfK] lipopeptide, which will enable the introduction of multifunctionality into c[RGDfK]-coated PLGA devices or nanoparticles.

The pore size of PLGA bone implants determines the de novo formation of bone tissue in tibial head defects in rats

PURPOSE

The influence of the pore size of biodegradable poly(lactic-co-glycolic acid) scaffolds on bone regeneration was investigated.

METHODS

Cylindrical poly(lactic-co-glycolic acid) scaffolds were implanted into a defect in the tibial head of rats. Pore sizes of 100-300, 300-500, and 500-710 μm were tested and compared to untreated defects as control. Two and four weeks after implantation, the specimens were explanted and defect regeneration and de novo extracellular matrix generation were investigated by MRI, quantitative solid-state NMR, and mass spectrometry.

RESULTS

The pore size of the scaffolds had a pronounced influence on the quantity of the extracellular matrix synthesized in the graft; most collagen was synthesized within the first 2 weeks of implantation, while the amount of hydroxyapatite increased in the second 2 weeks. After 4 weeks, the scaffolds contained large quantities of newly formed lamellar bone while the control defects were filled by inhomogenous woven bone. Best results were obtained for scaffolds of a pore size of 300-500 μm.

CONCLUSION

Our analysis showed that the structure and dynamics of the regenerated extracellular matrix was very similar to that of the native bone, suggesting that biomineralization was significantly enhanced by the choice of the most appropriate implant material.

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 characterization of chondrocyte cultures in plasma and whole blood biomatrices for cartilage tissue engineering

Many synthetic polymers and biomaterials have been used as matrices for 3D chondrocyte seeding and transplantation in the field of cartilage tissue engineering. To develop a fully autologous carrier for chondrocyte cultivation, we examined the feasibility of allogeneic plasma and whole blood-based matrices and compared them to agarose constructs. Primary articular chondrocytes isolated from 12-month-old pigs were embedded into agarose, plasma and whole blood matrices and cultivated under static-free swelling conditions for up to four weeks. To evaluate the quality of the synthesized extracellular matrix (ECM), constructs were subjected to weekly examinations using histological staining, spectrophotometry, immunohistochemistry and biochemical analysis. In addition, gene expression of cartilage-specific markers such as aggrecan, Sox9 and collagen types I, II and X was determined by RT-PCR. Chondrocyte morphology was assessed via scanning electron microscopy and viability staining, including proliferation and apoptosis assays. Finally, (13)  C NMR spectroscopy provided further evidence of synthesis of ECM components. It was shown that chondrocyte cultivation in allogeneic plasma and whole-blood matrices promoted sufficient chondrocyte viability and differentiation behaviour, resulting in neo-formation of a hyaline-like cartilage matrix.

Open porous microscaffolds for cellular and tissue engineering by lipid templating

Porous microspheres fabricated from biodegradable polymers have great potential as microscaffolds in tissue engineering applications, especially for novel strategies such as microtissue fabrication in vitro and microtissue assembly in vivo. Fabrication techniques for microparticulate scaffolds with surface and bulk pore sizes relevant for effective cell intrusion, however, are scarce. This study presents two techniques for the fabrication of open porous microscaffolds from poly(lactide-co-glycolide) in which lipid templating is used for pore formation and combined with either dispersion spraying or a double emulsion technique to determine the size and shape of the particulate structures generated. Both techniques yield microscaffolds with an average size of between 500 and 800 μm, high bulk porosities and open surface pores larger than 50 μm in diameter. Microscaffold morphology was investigated microscopically, particle size distribution was determined and porosity was quantified by intrusion measurements. Particle size and morphology was controlled by the processing parameters and the content and type of lipid porogen. Efficient extraction of the lipid template was shown by thermal analysis. Microscaffold cytocompatibility and in vitro cell culture performance was evaluated with L929 fibroblasts and rat adipose-derived stromal cells (ADSC), respectively. Extracts of different formulations were cytocompatible. Rat ADSC proliferated on the microscaffolds and were differentiated along the adipogenic lineage.