Classification of protein binding in hydroxyapatite chromatography: synergistic interactions on the molecular scale

Exploring preferred binding domains of IgG1 mAbs to multimodal adsorbents using a combined biophysics and simulation approach

In this work, we employ a recently developed biophysical technique that uses diethylpyrocarbonate (DEPC) covalent labeling and mass spectrometry for the identification of mAb binding patches to two multimodal cation exchange resins at different pH. This approach compares the labeling results obtained in the bound and unbound states to identify residues that are sterically shielded and thus located in the mAb binding domains. The results at pH 6 for one mAb (mAb B) indicated that while the complementarity determining region (CDR) had minimal interactions with both resins, the FC domain was actively involved in binding. In contrast, DEPC/MS data with another mAb (mAb C) indicated that both the CDR and FC domains were actively involved in binding. These results corroborated chromatographic retention data with these two mAbs and their fragments and helped to explain the significantly stronger retention of both the intact mAb C and its Fab fragment. In contrast, labeling results with mAb C at pH 7, indicated that only the CDR played a significant role in resin binding, again corroborating chromatographic data. The binding domains identified from the DEPC/MS experiments were also examined using protein surface hydrophobicity maps obtained using a recently developed sparse sampling molecular dynamics (MD) approach in concert with electrostatic potential maps. These results demonstrate that the DEPC covalent labeling/mass spectrometry technique can provide important information about the domain contributions of multidomain proteins such as monoclonal antibodies when interacting with multimodal resins over a range of pH conditions.

Harnessing ceramic hydroxyapatite as an effective polishing strategy to remove product- and process-related impurities in bispecific antibody purification

Bispecific antibody (bsAb), a novel therapeutic modality, provides excellent treatment efficacy, yet poses numerous challenges to downstream process development, which are mainly due to the intricate diversity of bsAb structures and impurity profiles. Ceramic hydroxyapatite (CHT), a mixed-mode medium, allows proteins to interact with its calcium sites (C-sites) through metal affinity and/or its phosphate sites (P-sites) through cation exchange interactions. This dual-binding capability potentially offers unique bind and elute behaviours for different proteins of interest, resulting in optimal product purity when suitable elution conditions are employed. In this study, the effectiveness of CHT as a polishing step for bsAb purification was investigated across three model molecules and benchmarked against the traditional cation exchange chromatography (CEX). For both asymmetric and symmetric IgG-like bsAb post Protein A eluates, at least 97% product purity was achieved after CHT polishing. CHT delivered a superior aggregate clearance to CEX, resulting in low high molecular weight (HMW) impurities (0.5%) and low process-related impurities in the product pools. Moreover, CHT significantly mitigated "chromatography-induced aggregation" whereas eightfold more HMW was generated by CEX. This study illustrated the developability of CHT in effectively eliminating low molecular weight (LMW) impurities through post-load-wash (PLW) optimization, resulting in an additional reduction of up to 48% in LMW impurities. A mechanistic explanation regarding the performance of impurity removal and mitigation of the chromatography-induced aggregation by CHT was proposed, illustrating unique CHT capability is potentially driven by C-site cooperation, of which effectiveness could depend on the bsAb composition and size.

Evaluation of preferred binding regions on ubiquitin and IgG1 FC for interacting with multimodal cation exchange resins using DEPC labeling/mass spectrometry

There is significant interest in identifying the preferred binding domains of biological products to various chromatographic materials. In this work, we develop a biophysical technique that uses diethyl pyrocarbonate (DEPC) based covalent labeling in concert with enzymatic digestion and mass spectrometry to identify the binding patches for proteins bound to commercially available multimodal (MM) cation exchange chromatography resins. The technique compares the changes in covalent labeling of the protein in solution and in the bound state and uses the differences in this labeling to identify residues that are sterically shielded upon resin binding and, therefore, potentially involved in the resin binding process. Importantly, this approach enables the labeling of many amino acids and can be carried out over a pH range of 5.5-7.5, thus enabling the protein surface mapping at conditions of interest in MM cation exchange systems. The protocol is first developed using the model protein ubiquitin and the results indicate that lysine residues located on the front face of the protein show dramatic changes in DEPC labeling while residues present on other regions have minimal or no reductions. This indicates that the front face of ubiquitin is likely involved in resin binding. In addition, surface property maps indicate that the hypothesized front face binding region consists of overlapping positively charged and hydrophobic patches. The technique is then employed with an IgG1 F_C and the results indicate that residues on the C_H 2-C_H 3 interface and the hinge are significantly sterically shielded upon binding to the resin. Further, these regions are again associated with significant overlap of positively charged and hydrophobic patches. On the other hand, while, residues on the C_H 2 and the front face of the IgG1 F_C also exhibited some changes in DEPC labeling upon binding, these regions have less distinct charged and hydrophobic patches. Importantly, the hypothesized binding patches identified for both ubiquitin and F_C using this approach are shown to be consistent with previously reported NMR studies. In contrast to NMR, this new approach enables the identification of preferred binding regions without the need for isotopically labeled proteins or chemical shift assignments. The technique developed in this work sets the stage for the evaluation of the binding domains of a wide range of biological products to chromatographic surfaces, with important implications for designing biomolecules with improved biomanufacturability properties.

Role of nanostructured materials in hard tissue engineering

The rise in the use of biomaterials in bone regeneration in the last decade has exponentially multiplied the number of publications, methods, and approaches to improve and optimize their functionalities and applications. In particular, biomimetic strategies based on the self-assembly of molecules to design, create and characterize nanostructured materials have played a very relevant role. We address this idea on four different but related points: self-setting bone cements based on calcium phosphate, as stable tissue support and regeneration induction; metallic prosthesis coatings for cell adhesion optimization and prevention of inflammatory response exacerbation; bio-adhesive hybrid materials as multiple drug delivery localized platforms and finally bio-inks. The effect of the physical, chemical, and biological properties of the newest biomedical devices on their bone tissue regenerative capacity are summarized, described, and analyzed in detail. The roles of experimental conditions, characterization methods and synthesis routes are emphasized. Finally, the future opportunities and challenges of nanostructured biomaterials with their advantages and shortcomings are proposed in order to forecast the future directions of this field of research.

Advanced Materials Based on Nanosized Hydroxyapatite

The development of new materials based on hydroxyapatite has undergone a great evolution in recent decades due to technological advances and development of computational techniques. The focus of this review is the various attempts to improve new hydroxyapatite-based materials. First, we comment on the most used processing routes, highlighting their advantages and disadvantages. We will now focus on other routes, less common due to their specificity and/or recent development. We also include a block dedicated to the impact of computational techniques in the development of these new systems, including: QSAR, DFT, Finite Elements of Machine Learning. In the following part we focus on the most innovative applications of these materials, ranging from medicine to new disciplines such as catalysis, environment, filtration, or energy. The review concludes with an outlook for possible new research directions.

Nanostructure of bioactive glass affects bone cell attachment via protein restructuring upon adsorption

The nanostructure of engineered bioscaffolds has a profound impact on cell response, yet its understanding remains incomplete as cells interact with a highly complex interfacial layer rather than the material itself. For bioactive glass scaffolds, this layer comprises of silica gel, hydroxyapatite (HA)/carbonated hydroxyapatite (CHA), and absorbed proteins—all in varying micro/nano structure, composition, and concentration. Here, we examined the response of MC3T3-E1 pre-osteoblast cells to 30 mol% CaO–70 mol% SiO₂ porous bioactive glass monoliths that differed only in nanopore size (6–44 nm) yet resulted in the formation of HA/CHA layers with significantly different microstructures. We report that cell response, as quantified by cell attachment and morphology, does not correlate with nanopore size, nor HA/CHO layer micro/nano morphology, or absorbed protein amount (bovine serum albumin, BSA), but with BSA’s secondary conformation as indicated by its β-sheet/α-helix ratio. Our results suggest that the β-sheet structure in BSA interacts electrostatically with the HA/CHA interfacial layer and activates the RGD sequence of absorbed adhesion proteins, such as fibronectin and vitronectin, thus significantly enhancing the attachment of cells. These findings provide new insight into the interaction of cells with the scaffolds’ interfacial layer, which is vital for the continued development of engineered tissue scaffolds.

Inorganic Porous Bulk Discs as a Matrix for Thin-Layer Chromatography and Translucent Hard Composite Materials

Magnesium-stabilized amorphous calcium carbonate (Mg-ACC), amorphous magnesium calcium silicate hydrate (MCSH), and hydroxyapatite (HAp) are prepared by a precipitation method. By cold-pressing these particles, it is possible to produce porous bulk discs with a narrow pore size distribution. These porous inorganic discs (Mg-ACC, MCSH, and HAp) are investigated as stationary phases to study the chromatographic behavior and adsorption ability of rhodamine B, methylene blue, and ribonuclease. The adsorption affinities of different biomolecules can be easily observed and evaluated through this method. Furthermore, by infiltrating fabricated opaque porous discs with benzyl ether, which has a similar refractive index as the used inorganic particles (Mg-ACC, MCSH, and HAp), their optical properties significantly change and the discs become translucent. Moreover, by infiltrating the MCSH discs with a light-curing polymer, translucent composites with good surface hardness are fabricated. By doping particles with ions such as Ni²⁺, Co²⁺, Fe³⁺, and Eu³⁺, the color and UV-visible spectrum of the bulk discs can be adjusted. Typically, by using iron-doped MCSH particles as the inorganic matrix, nanocomposites, which show a steep UV-absorption edge at 400 nm, are fabricated. Our work provides a simple and economical method to evaluate the affinity of biomolecules to inorganic materials and a novel way to fabricate translucent hard composite materials. The fabricated nanocomposite discs show a great UV shielding effect and superior surface hardness compared to polymethyl methacrylate and commercial sunglasses, suggesting their potential as new sunglass materials.

Retention Mechanism of Proteins in Hydroxyapatite Chromatography - Multimodal Interaction Based Protein Separations: A Model Study

BACKGROUND

Retention mechanism of proteins in hydroxyapatite chromatography (HAC) was investigated by linear gradient elution experiments (LGE).

MATERIALS AND METHODS

Several mobile phase (buffer) solution strategies and solutes were evaluated in order to probe the relative contributions of two adsorption sites of hydroxyapatite (HA) particles, C-site due to Ca (metal affinity) and P-site due to PO4 (cation-exchange). When P-site was blocked, two basic proteins, lysozyme (Lys) and ribonuclease A(RNase), were not retained whereas cytochrome C(Cyt C) and lactoferrin (LF) were retained and also retention of acidic proteins became stronger as the repulsion due to P-site was eliminated. The number of the binding site B values determined from LGE also increased, which also showed reduction of repulsion forces.

CONCLUSION

The selectivity (retention) of four basic proteins (RNase, Lys, Cyt C, LF) in HAC was different from that in ion-exchange chromatography. Moreover, it was possible to tune the selectivity by using NaCl gradient.

Hydroxyapatite nanoparticle based fluorometric determination and imaging of cysteine and homocysteine in living cells

Fluorescent hydroxyapatite nanoparticles (HAP-NPs) were prepared by reacting calcium ion with phosphate in the presence of Eu(III) ion. The HAP-NPs display large Stokes' shift and two strong fluorescence emissions with peaks at 590 nm and 615 nm when excited at 250 nm. The HAP-NPs also have good photostability and water solubility. The HAP-NPs combined with Cu(II) were applied to fluorometric determination of cysteine and homocysteine in biological samples and in living cells. In this detection scheme, the fluorescence of HAP-NPs is initially quenched by Cu(II). The addition of biothiols results in the formation of Cu(II)-thiol complexes and leads to fluorescence recovery. The assay allows cysteine to be detected with a 110 nM detection limit, and homocysteine with a 160 nM detection limit. The assay was successfully applied to the analysis of cysteine in spiked human serum samples and to imaging of cysteine in HeLa cells, and this demonstrates its potential for clinical testing and in biomedical research. Graphical abstract Fluorescent hydroxyapatite nanoparticles were synthesized and combined with Cu²⁺ for fluorescence sensing of biothiols (cysteine and homocysteine) in complex biological samples and in living cells.

Facile covalent bio-conjugation of hydroxyapatite

A facile covalent bio-conjugation of hydroxyapatite has been developed and employed for the conjugation of hydrophobic proteins.

Calcium orthophosphates (CaPO4): occurrence and properties

The present overview is intended to point the readers' attention to the important subject of calcium orthophosphates (CaPO4). This type of materials is of the special significance for the human beings because they represent the inorganic part of major normal (bones, teeth and antlers) and pathological (i.e., those appearing due to various diseases) calcified tissues of mammals. For example, atherosclerosis results in blood vessel blockage caused by a solid composite of cholesterol with CaPO4, while dental caries and osteoporosis mean a partial decalcification of teeth and bones, respectively, that results in replacement of a less soluble and harder biological apatite by more soluble and softer calcium hydrogenorthophosphates. Therefore, the processes of both normal and pathological calcifications are just an in vivo crystallization of CaPO4. Similarly, dental caries and osteoporosis might be considered as in vivo dissolution of CaPO4. In addition, natural CaPO4 are the major source of phosphorus, which is used to produce agricultural fertilizers, detergents and various phosphorus-containing chemicals. Thus, there is a great significance of CaPO4 for the humankind and, in this paper, an overview on the current knowledge on this subject is provided.

Bone protein extraction without demineralization using principles from hydroxyapatite chromatography

Historically, extraction of bone proteins has relied on the use of demineralization to better retrieve proteins from the extracellular matrix; however, demineralization can be a slow process that restricts subsequent analysis of the samples. Here, we developed a novel protein extraction method that does not use demineralization but instead uses a methodology from hydroxyapatite chromatography where high concentrations of ammonium phosphate and ammonium bicarbonate are used to extract bone proteins. We report that this method has a higher yield than those with previously published small-scale extant bone extractions, with and without demineralization. Furthermore, after digestion with trypsin and subsequent high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis, we were able to detect several extracellular matrix and vascular proteins in addition to collagen I and osteocalcin. Our new method has the potential to isolate proteins within a short period (4h) and provide information about bone proteins that may be lost during demineralization or with the use of denaturing agents.

Hydroxyapatite nanocrystals: colloidal chemistry, assembly and their biological applications

In this review, recent advances in the tunable synthesis, ion doping, assembly and applications of monodisperse HAp nanocrystals are summarized.

Single-step inline hydroxyapatite enrichment facilitates identification and quantitation of phosphopeptides from mass-limited proteomes with MudPIT

Herein we report the characterization and optimization of single-step inline enrichment of phosphopeptides directly from small amounts of whole cell and tissue lysates (100-500 μg) using a hydroxyapatite (HAP) microcolumn and Multidimensional Protein Identification Technology (MudPIT). In comparison to a triplicate HILIC-IMAC phosphopeptide enrichment study, ∼80% of the phosphopeptides identified using HAP-MudPIT were unique. Similarly, analysis of the consensus phosphorylation motifs between the two enrichment methods illustrates the complementarity of calcium- and iron-based enrichment methods and the higher sensitivity and selectivity of HAP-MudPIT for acidic motifs. We demonstrate how the identification of more multiply phosphorylated peptides from HAP-MudPIT can be used to quantify phosphorylation cooperativity. Through optimization of HAP-MudPIT on a whole cell lysate we routinely achieved identification and quantification of ca. 1000 phosphopeptides from a ∼1 h enrichment and 12 h MudPIT analysis on small quantities of material. Finally, we applied this optimized method to identify phosphorylation sites from a mass-limited mouse brain region, the amygdala (200-500 μg), identifying up to 4000 phosphopeptides per run.