How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations

Reinforced dentin remineralization via a novel dual-affinity peptide

OBJECTIVES

In light of the constantly flowing saliva, anti-caries remineralization agents are inclined to be taken away. Owing to their limited residence time, the remineralization effect is not as desirable as expected. Hence, our study aimed to synthesize a novel peptide (DGP) with high affinity to both collagen fibrils and hydroxyapatite, and investigated its dentin remineralization efficacy in vitro and anti-caries capability in vivo.

METHODS

DGP was synthesized through Fmoc solid-phase reaction. The binding ability and interaction mechanism of DGP to demineralized dentin were investigated. Dentin specimens were demineralized, then treated with DGP and deionized water respectively. The specimens were incubated in artificial saliva and in-vitro remineralization effectiveness was analyzed after 14 days. The rat caries model was established to further scrutinize the in-vivo efficacy of caries prevention.

RESULTS

DGP possesses an enhanced adhesion force of 12.29 ± 1.12 nN to demineralized dentin. The favorable adsorption capacity is ascribed to the stable hydrogen bonds between S2P-101 and ASP-100 of DGP and GLY33 and PRO-16 of collagen fibers. Abundant mineral deposits and remarkable tubule occlusion were observed in the DGP group. DGP-treated dentin obtained notable microhardness recovery and higher mineral content after a 14-day remineralization regimen. DGP also demonstrated potent caries prevention in vivo, with substantially fewer carious lesions and significantly lower Keyes scoring.

SIGNIFICANCE

DGP proves to possess a high affinity to demineralized dentin regardless of saliva flowing, thus enhancing remineralization potency significantly in vitro and in vivo, potential for dental caries prevention and combatting initial dentin caries clinically.

Small organic molecules containing amorphous calcium phosphate: synthesis, characterization and transformation

As the primary solid phase, amorphous calcium phosphate (ACP) is a pivotal precursor in cellular biomineralization. The intrinsic interplay between ACP and Howard factor underscores the significance of understanding their association for advancing biomimetic ACP development. While organic compounds play established roles in biomineralization, this study presents the synthesis of ACP with naturally occurring organic compounds (ascorbate, glutamate, and itaconate) ubiquitously found in mitochondria and vital for bone remodeling and healing. The developed ACP with organic compounds was meticulously characterized using XRD, FTIR, and solid-state 13C and 31P NMR. The morphological analysis revealed the characteristic spherical morphology with particle size close to 20 nm of all synthesized ACP variants. Notably, the type of organic compound strongly influences true density, specific surface area, particle size, and transformation. The in vitro analysis was performed with MC3T3-E1 cells, indicating the highest cell viability with ACP_ASC (ascorbate), followed by ACP_ITA (itaconate). The lowest cell viability was observed with 10 %w/v of ACP_GLU (glutamate); however, 1 %w/v of ACP_GLU was cytocompatible. Further, the effect of small organic molecules on the transformation of ACP to low crystalline apatite (Ap) was examined in Milli-Q® water, PBS, and α-MEM.

Nucleation Domains in Biomineralization: Biomolecular Sequence and Conformational Features

Biomolecules play a vital role in the regulation of biomineralization. However, the characteristics of practical nucleation domains are still sketchy. Herein, the effects of the representative biomolecular sequence and conformations on calcium phosphate (Ca-P) nucleation and mineralization are investigated. The results of computer simulations and experiments prove that the line in the arrangement of dual acidic/essential amino acids with a single interval (Bc (Basic) -N (Neutral) -Bc-N-Ac (Acidic)- NN-Ac-N) is most conducive to the nucleation. 2α-helix conformation can best induce Ca-P ion cluster formation and nucleation. "Ac- × × × -Bc" sequences with α-helix are found to be the features of efficient nucleation domains, in which process, molecular recognition plays a non-negligible role. It further indicates that the sequence determines the potential of nucleation/mineralization of biomolecules, and conformation determines the ability of that during functional execution. The findings will guide the synthesis of biomimetic mineralized materials with improved performance for bone repair.

Parameter Dependence of the Solubility Limit for Disodium Phosphate

The solubility limit was calculated for supersaturated solutions of disodium phosphate in water as a function of the sodium-oxygen Lennard-Jones radius parameter Rmin. We found that changes in the sodium-oxygen Rmin were clearly exponentially related to the concentration of the solubility limit. Starting from standard force fields more suited to nucleic acids and phospholipids, only relatively small changes were required to achieve the experimentally known solubility limit. Simultaneously, we found that it was possible to achieve the solubility limit and the osmotic pressure with the same model parameters. Based on transferability, the adjusted Rmin parameter can be used to more accurately model phosphorylated proteins.

Advances in biomimetic collagen mineralisation and future approaches to bone tissue engineering

With an ageing world population and ~20% of adults in Europe being affected by bone diseases, there is an urgent need to develop advanced regenerative approaches and biomaterials capable to facilitate tissue regeneration while providing an adequate microenvironment for cells to thrive. As the main components of bone are collagen and apatite mineral, scientists in the tissue engineering field have attempted in combining these materials by using different biomimetic approaches to favour bone repair. Still, an ideal bone analogue capable of mimicking the distinct properties (i.e., mechanical properties, degradation rate, porosity, etc.) of cancellous bone is to be developed. This review seeks to sum up the current understanding of bone tissue mineralisation and structure while providing a critical outlook on the existing biomimetic strategies of mineralising collagen for bone tissue engineering applications, highlighting where gaps in knowledge exist.

Sustained local ionic homeostatic imbalance caused by calcification modulates inflammation to trigger heterotopic ossification

Heterotopic ossification (HO) is a condition triggered by an injury leading to the formation of mature lamellar bone in extraskeletal soft tissues. Despite being a frequent complication of orthopedic and trauma surgery, brain and spinal injury, the etiology of HO is poorly understood. The aim of this study is to evaluate the hypothesis that a sustained local ionic homeostatic imbalance (SLIHI) created by mineral formation during tissue calcification modulates inflammation to trigger HO. This evaluation also considers the role SLIHI could play for the design of cell-free, drug-free osteoinductive bone graft substitutes. The evaluation contains five main sections. The first section defines relevant concepts in the context of HO and provides a summary of proposed causes of HO. The second section starts with a detailed analysis of the occurrence and involvement of calcification in HO. It is followed by an explanation of the causes of calcification and its consequences. This allows to speculate on the potential chemical modulators of inflammation and triggers of HO. The end of this second section is devoted to in vitro mineralization tests used to predict the ectopic potential of materials. The third section reviews the biological cascade of events occurring during pathological and material-induced HO, and attempts to propose a quantitative timeline of HO formation. The fourth section looks at potential ways to control HO formation, either acting on SLIHI or on inflammation. Chemical, physical, and drug-based approaches are considered. Finally, the evaluation finishes with a critical assessment of the definition of osteoinduction. STATEMENT OF SIGNIFICANCE: The ability to regenerate bone in a spatially controlled and reproducible manner is an essential prerequisite for the treatment of large bone defects. As such, understanding the mechanism leading to heterotopic ossification (HO), a condition triggered by an injury leading to the formation of mature lamellar bone in extraskeletal soft tissues, would be very useful. Unfortunately, the mechanism(s) behind HO is(are) poorly understood. The present study reviews the literature on HO and based on it, proposes that HO can be caused by a combination of inflammation and calcification. This mechanism helps to better understand current strategies to prevent and treat HO. It also shows new opportunities to improve the treatment of bone defects in orthopedic and dental procedures.

Molecular dynamic simulation of prenucleation of apatite at a type I collagen template: ion association and mineralization control

Biomineralization is a vital physiological process in living organisms, hence elucidating its mechanism is crucial in the optimization of controllable biomaterial preparation with hydroxyapatite and collagen, which could provide information for the design of innovative biomaterials. However, the mechanisms by which minerals and collagen interact in various ionic environments are unclear. Here, we applied molecular dynamics and free energy simulations to clarify type I collagen-mediated HAP prenucleation and simulated the physiological environment using different phosphate and carbonate protonation states. Calcium phosphate mineral formation on the type I collagen surface drastically differed among various H₂PO₄^-, HPO₄^2-, PO₄^3-, CO₃^2-, and HCO₃^- compositions. Our simulations indicated that the presence of HPO₄^2- in the solution phase is critical to regulate the apatite nucleation, whereas the presence of H₂PO₄^- may be inhibitory. The inclusion of CO₃^2- in the solution might promote calcium phosphate cluster formation. In contrast, apatite cluster size may be regulated by changing the anion concentration ratios, including PO₄^3-/HPO₄^2- and PO₄^3-/CO^32-. Our free energy simulations attributed these phenomena to relative differences in binding thermostability and ion association kinetics. Our simulations provide a theoretical approach toward the effective control of collagen mineralization and the preparation of novel biomaterials.

Biomineralization from the Perspective of Ion Aggregation: Calcium Phosphate Nucleation in the Physiological Environment

Biomineralization is an important process of bone tissue generation. Calcium (Ca) and phosphate (P) ions aggregate and nucleate under the regulation of biomolecules at the initial mineralization stage. Due to the complexity of the physiological environment, the movement behavior and mineralization mechanism of calcium and phosphate ions, as well as the effect of biomolecules on them, are not clear. In this study, computer simulations and experimental verification were applied to investigate the characteristics of the initial biomineralization from the view of ion aggregation and nucleation. The results prove that P ions play a more important role in mineralization than Ca ions. The guanidyl group and surrounding carboxyl terminal groups are a potential excellent nucleation domain on proteins. The interval distribution of acidic/basic residues on protein is more conductive to the formation of large Ca and P ions clusters. The involvement of protein could increase the probability of hydroxyapatite phase precipitation, especially in the presence of a helical conformation. The detailed information on Ca and P ions behavior provided by the computer simulations is helpful for further understanding the mechanism of biomineralization, which will promote the development of bone repair materials to the biomimetic mineralized materials.

Molecular Dynamics Exploration of the Growth Mechanism of Hydroxyapatite Nanoparticles Regulated by Glutamic Acid

Morphological control can enhance the performance of materials like hydroxyapatite (HAP), a well-known bioceramic with various morphologies, including spheres, rods, whiskers, needles, and plates. To obtain certain HAP morphologies, the crystal growth mechanisms at different planes should be investigated. Here, molecular dynamics was employed to understand the mechanism of HAP nanoparticle growth regulated by glutamic acid (Glu). Long-time dynamics simulations and free energy calculations were performed to explore the effect of Glu on calcium and phosphate ion precipitation on the HAP (100) and (001) faces. Without Glu, PO₄^3- prefers binding to the HAP (100) surface, whereas with Glu, the (001) surface is preferred. This could partially explain why HAP changes from needle-like to plate-like with Glu addition in experiments. Our theoretical results indicate that Glu inhibits calcium and phosphate ion deposition on the crystal surfaces by occupying the calcium sites on the outermost layers. In addition, Glu has a strong concentration gradient effect on HAP deposition. At Glu concentrations of >80 mM, ion deposition was inhibited more on the (100) than on the (001) surface. Our results agree with experimental observations and afford insights into complicated HAP crystal growth mechanisms with foreign additives, which will aid in HAP synthesis with morphological control.

Simulation Insight into the Synergic Role of Citrate and Polyaspartic Peptide in Biomineralization

Hydroxyapatite (HAP) is one of the most important inorganic components in biological minerals such as bones and teeth. More than 90% of the total citrate is accumulated in human bones and other biomineralized tissues. In addition, mineralizing proteins are enriched in glutamate and aspartate residues, which are important for their mineral-regulating properties. However, how citrate ions (CITs) and/or acidic amino acids regulate the formation of HAP is still unclear. In this work, molecular dynamics simulations were performed to study how CIT regulates the adsorption behavior of polyaspartic acid (PASP) on the HAP surface in the calcium phosphate solution. The simulation results indicate that PASP can be used as an ion chelator to complex Ca²⁺ and can serve as templates for HAP mineralization by templating the distribution of Ca²⁺ on its surface, which are attributed to the -COO^- and α-helix structure. Most importantly, the orientation distributions of PASP in all systems are narrower with the help of CIT, thereby PASP can be adsorbed on the HAP surface stably with a "lying-down" orientation. This indicates that CIT can be used as a bridging agent to bond the acidic peptide to the HAP surface in biomineralization. Thus, the synergic role of CIT and the acidic peptide on the HAP surface were revealed in this work, which can provide new insights into the interfacial phenomena during the biomineralization.

Electric Field-Mediated Fibronectin-Hydroxyapatite Interaction: A Molecular Insight

In experimental research-driven biomaterials science, the influence of different material properties (elastic stiffness, surface energy, etc.) and, to a relatively lesser extent, biophysical stimulation (electric/magnetic) on cell-material interactions has been extensively investigated. Despite the central importance of protein adsorption on cell-material interactions, the quantitative analysis to probe into the role of physicochemical factors in protein adsorption remains largely unexplored in biomaterials science. In recent studies, the critical role of electric field stimulation toward the modulation of cell functionality in implantable biomaterials has been experimentally demonstrated. Given this background, we investigated the influence of external electric field stimulation (upto 1.00 V/nm) on fibronectin (FN) adsorption on a hydroxyapatite (HA) (001) surface at 300 K using the all-atom molecular dynamics (MD) simulation method. FN adsorption was found to be governed by attractive electrostatic interactions, which changed with the electric field strength. Nonmonotonous changes in the structural integrity of FN were recorded with the change in the field strength and direction. This can be attributed to the spatial rearrangement of the positions of local charges and the global structural changes of proteins. The dipole moment vectors of FN, water, and HA quantitatively exhibited a similar pattern of orienting themselves parallel to the field direction, with field strength-dependent increase in their magnitudes. No significant change has been recorded for the radial distribution function of water surrounding FN. Field-dependent variation in the salt bridge nets and the number of hydrogen bonds between FN and HA were also examined. One of the important results in the context of cell-material interaction is that the RGD (Arg-Gly-Asp) sequence of FN was exposed to the solvent side when the field was applied along an outward direction perpendicular to the HA (001) surface. In summary, the present study provides molecular insights into the influence of electric field stimulation on phenomenological interactions involved in FN adsorption on the HA surface.

Oligo(l-glutamic acids) in Calcium Phosphate Precipitation: Mechanism of Delayed Phase Transformation

Proteins and their mimics that contain negatively charged sequences are important in natural and biomimetic mineralization. The mechanism by which these sequences affect calcium phosphate mineralization is not well understood. Here, peptides containing different numbers of repeat units of contiguous glutamic acid residues, oligo(l-glutamic acid)_n (n = 3, 7, 8, 10), were investigated with regards to the mechanism in delaying the crystallization of amorphous calcium phosphate (ACP) while holding the amount of carboxylic acid groups in solution constant. Increasing peptide chain length increases the stability of ACP at a certain total amount of carboxylic acid groups in solution. This effect is shown to be due to stronger binding as well as binding to more calcium ions per peptide by the longer oligopeptides compared to the shorter ones. It is proposed that these associations delay the structural rearrangement of calcium ions and the dehydration of ACP, which are required for the crystallization of hydroxyapatite. The initial nucleation and the local structure of ACP, however, do not vary with chain length. This second part of a two-part series provides an improved mechanistic understanding of how organic additives, especially those with contiguous acidic amino acid sequences, modulate the kinetics of calcium phosphate precipitation and phase transformation.

Toward the Understanding of Small Protein-Mediated Collagen Intrafibrillar Mineralization

The design of improved materials for orthopedic implants and bone tissue engineering scaffolds relies on materials mimicking the properties of bone. Calcium phosphate (Ca-PO₄)-mineralized collagen fibrils arranged in a characteristic hierarchical structure constitute the building blocks of mineralized vertebrate tissues and control their biomechanical and biochemical properties. Large, flexible, acidic noncollagenous proteins (ANCPs) have been shown to influence collagen mineralization but little is known about mineralization mechanisms with the aid of small proteins. Osteocalcin (OCN) is a small, highly structured biomolecule known as a multifunctional hormone in its undercarboxylated form. Here, we examined the potential mechanism of collagen intrafibrillar mineralization in vitro mediated by OCN as a model protein. Rapid and random extrafibrillar mineralization of flakey Ca-PO₄ particles was observed by transmission electron microscopy mainly on the outer surfaces of collagen fibrils of a preformed collagen scaffold in the absence of the protein. In contrast, the protein stabilized hydrated, spherical nanoclusters of Ca-PO₄ on the outer surface of the fibrils, thereby retarding extrafibrillar mineralization. The nanoclusters then infiltrated the fibrils resulting in intrafibrillar mineralization with HAP crystals aligned with the fibrils. This mechanism is similar to that observed for unstructured ANCPs. Results of fibrillogenesis and immunogold labeling studies showed that OCN was associated primarily with the fibrils, consistent with ex vivo studies on mineralizing turkey tendon. The present findings contribute to expanding our understanding of collagen intrafibrillar mineralization and provide insight into design synthetic macromolecular matrices for orthopedic implants and bone regeneration.

Osteocalcin is necessary for the alignment of apatite crystallites, but not glucose metabolism, testosterone synthesis, or muscle mass

The strength of bone depends on bone quantity and quality. Osteocalcin (Ocn) is the most abundant noncollagenous protein in bone and is produced by osteoblasts. It has been previously claimed that Ocn inhibits bone formation and also functions as a hormone to regulate insulin secretion in the pancreas, testosterone synthesis in the testes, and muscle mass. We generated Ocn-deficient (Ocn^–/–) mice by deleting Bglap and Bglap2. Analysis of Ocn^–/–mice revealed that Ocn is not involved in the regulation of bone quantity, glucose metabolism, testosterone synthesis, or muscle mass. The orientation degree of collagen fibrils and size of biological apatite (BAp) crystallites in the c-axis were normal in the Ocn^–/–bone. However, the crystallographic orientation of the BAp c-axis, which is normally parallel to collagen fibrils, was severely disrupted, resulting in reduced bone strength. These results demonstrate that Ocn is required for bone quality and strength by adjusting the alignment of BAp crystallites parallel to collagen fibrils; but it does not function as a hormone.

The strength of bone depends on both its quantity and quality. Osteocalcin (Ocn) is the most abundant non-collagenous protein in bone, but its function remains unclear. Earlier studies by other investigators have suggested that Ocn decreases the quantity of bone by decreasing bone formation; and in addition it works as a hormone to regulate glucose metabolism, testosterone synthesis, and muscle mass in distant tissues. We have generated Ocn-deficient mice and show herein that Ocn is not required for bone formation. It is, however, required for optimal bone quality and strength. Specifically, we show that in the Ocn-deficient mice collagen fibers align normally, but apatite crystallites align randomly against collagen, resulting in disorganized mineralization and reduced bone strength. Furthermore, we show that glucose metabolism, testosterone synthesis, and muscle mass are normal in the Ocn-deficient mice. We conclude that Ocn acts in bone to optimize its quality and strength, but not quantity. And, in contrast to earlier claims, it does not work as a hormone to control glucose metabolism, testosterone synthesis, and muscle mass.

Structure-Activity Relationships of Hydroxyapatite-Binding Peptides

Elucidating the structure-activity relationships between biomolecules and hydroxyapatite (HAP) is essential to understand bone mineralization mechanisms, develop HAP-based implants, and design drug delivery vectors. Here, four peptides identified by phage display were selected as model HAP-binding peptides (HBPs) to examine the effects of primary amino acid sequence, phosphorylation of serine, presence of charged amino acid residues, and net charge of the peptide on (1) HAP-binding affinity, (2) secondary conformation, and (3) HAP nucleation and crystal growth. Binding affinities were determined by obtaining adsorption isotherms by mass depletion, and the conformations of the peptides in solution and bound states were observed by circular dichroism. Results showed that the magnitude of the net charge primarily controlled binding affinity, with little dependence on the other HBP features. The binding affinity and conformation results were in good agreement with our previous molecular dynamics simulation results, thus providing an excellent benchmark for the simulations. Transmission electron microscopy was used to explore the effect of these HBPs on calcium phosphate (Ca-PO₄) nucleation and growth. Results indicated that HBPs may inhibit nucleation of Ca-PO₄ nanoparticles and their phase transition to crystalline HAP, as well as control crystal growth rates in specific crystallographic directions, thus changing the classical needle-like morphology of inorganically grown HAP crystals to a biomimetic plate-like morphology.

Proteins, peptides and peptidomimetics as active agents in implant surface functionalization

The recent impact of implants on improving the human life quality has been enormous. During the past two decades we witnessed major advancements in both material and structural development of implants. They were driven mainly by the increasing patients' demand and the need to address the major issues that come along with the initially underestimated complexity of the bone-implant interface. While both, the materials and design of implants reached a certain, balanced state, recent years brought a shift in focus towards the bone-implant interface as the weakest link in the increasing implant long-term usability. As a result, several approaches were developed. They aimed at influencing and enhancing the implant osseointegration and its proper behavior when under load and stress. With this review, we would like to discuss the recent advancements in the field of implant surface modifications, emphasizing the importance of chemical methods, focusing on proteins, peptides and peptidomimetics as promising agents for titanium surface coatings.

Bioinspired by both mussel foot protein and bone sialoprotein: universal adhesive coatings for the promotion of mineralization and osteogenic differentiation

Natural protein bioinspired coatings are developed to promote the mineralization and osteogenic differentiation of MC3T3-E1 cells for implant material use.

Natural protein bioinspired materials for regeneration of hard tissues

This review describes the protein bioinspired materials for the repair of hard tissues such as enamel, dentin and bone.

Hydroxyapatite Formation on Self-Assembling Peptides with Differing Secondary Structures and Their Selective Adsorption for Proteins

Self-assembling peptides have been employed as biotemplates for biomineralization, as the morphologies and sizes of the inorganic materials can be easily controlled. We synthesized two types of highly ordered self-assembling peptides with different secondary structures and investigated the effects of secondary structures on hydroxyapatite (HAp) biomineralization of peptide templates. All as-synthesized HAp-peptides have a selective protein adsorption capacity for basic protein (e.g., cytochrome c and lysozyme). Moreover, the selectivity was improved as peptide amounts increased. In particular, peptide-HAp templated on β-sheet peptides adsorbed more cytochrome c than peptide-HAp with α-helix structures, due to the greater than 2-times carboxyl group density at their surfaces. It can be expected that self-assembled peptide-templated HAp may be used as carriers for protein immobilization in biosensing and bioseparation applications and as enzyme-stabilizing agents.

Silk fibroin-derived polypeptides additives to promote hydroxyapatite nucleation in dense collagen hydrogels

Silk fibroin-derived polypeptides (FDPs) are polypeptides resulting from the enzymatic separation of the hydrophobic crystalline (Cp) and hydrophilic electronegative amorphous (Cs) components of silk fibroin (SF). The role of these polypeptides in promoting the nucleation of hydroxyapatite (HA) has been previously investigated, yet is still not fully understood. Here we study the potential of HA mineralization via FDPs incorporated at 1:10, 1:2 and 1:1 in a plastically compressed (PC) and dense collagen (DC) scaffold. Scaffolds were immersed in simulated body fluid (SBF) at physiological conditions (pH = 7.4, 37°C) to promote biomineralization. The effect of Cs and Cp to promote HA nucleation was investigated at different time points, and compared to pure DC scaffolds. Characterization of Cs and Cp fragments using Liquid Chromatography-Mass Spectrometry (LCMS) showed little difference in the amino acid composition of the FDPs. Results obtained in vitro using Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM) X-Ray Diffraction (XRD) and mass analysis showed little difference between scaffolds that incorporated Cs, Cp, and DC hydrogels. These results demonstrated that silk FDPs incorporation are not yet suitable to promote HA nucleation in vivo without further refining the collagen-FDP system.

Correlations between gene expression and mineralization in the avian leg tendon

Certain avian tendons have been studied previously as a model system for normal mineralization of vertebrates in general. In this regard, the gastrocnemius tendon in the legs of turkeys mineralizes in a well defined temporal and spatial manner such that changes in the initial and subsequent events of mineral formation can be associated with time and specific locations in the tissue. In the present investigation, these parameters and mineral deposition have been correlated with the expression of several genes and the synthesis and secretion of their related extracellular matrix proteins by the composite tenocytes of the tendon. Quantitative polymerase chain reaction analysis demonstrates that mRNA expression of the non-collagenous genes of bone sialoprotein, osteopontin, and osteocalcin corresponds well with the temporal and spatial onset and progression of mineralization. Immunolocalization separately confirms the synthesis and secretion of these matrix molecules. The expression of other non-collagenous genes such as decorin does not show strong correlation with turkey leg tendon mineralization, and expression of vimentin, a cytoskeletal component which may be regulated by biomechanical factors in the tendon, may lead to inhibition of osteocalcin expression during the development and mineralization of the tissue. The overall results of this work provide insight into direct temporal and spatial relations between the genes and proteins of interest as well as the formation and deposition of mineral in the avian tendon model.

Physical origin underlying the prenucleation-cluster-mediated nonclassical nucleation pathways for calcium phosphate

The involvement of prenucleation clusters (PNCs) in crystallization from a supersaturated solution has been recently admitted within the framework of nonclassical nucleation theory; however, little is known about PNCs, at the quantitative level, for their formation mechanism and stability, the new phase formed by them, as well as their impact on nucleation barriers. Herein, using the sophisticated free energy calculations with a cumulative simulation time of over 5 μs, we identify a thermodynamically favored pathway of the PNC-mediated nucleation for calcium phosphate, starting with the ion pair association in solution. We demonstrate that such an ion association occurs not only between cations and anions, but also for the polyatomic species with charges of the same sign, which, in fact, leads to PNC formation via the consecutive coordination of the phosphate ions to calcium. The free energy decomposition calculations illustrate that the water phase is capable to either hinder or promote ion association for the abovementioned processes, and its specific role is intricately related to the characteristics of the hydration shell around calcium ions. The favorable interactions between the highly charged species play a crucial role in stabilizing the PNC complexes and the aggregates formed by PNCs. Furthermore, our present work reveals that the uptake of an extra calcium ion is the first and mandatory step to trigger PNC aggregation into amorphous calcium phosphate (ACP) by eliminating the related free energy barriers. Our theoretical study successfully provides quantitative explanations to a large set of experimental data in the field, which is currently under intense discussions associated with the nonclassical nucleation mechanism. The combination of computational methods developed in our present work offers a feasible and general solution to quantitatively and systematically study ion associations and crystal nucleation/growth in an aqueous solution at the atomic level, which are normally inaccessible to most of the existing experimental acquisitions.

Computer simulations of the adsorption of an N-terminal peptide of statherin, SN15, and its mutants on hydroxyapatite surfaces

Salt-bridge adsorption of the SN15 peptide and its mutants on the HAP(001) surface.

Specific matrix metalloproteinases and calcification factors are associated with the vulnerability of human carotid plaque

The rupture of atherosclerotic plaque provokes the majority of acute cerebrovascular events. Studies have demonstrated that various matrix metalloproteinases (MMPs) may promote atherosclerotic plaque progression and rupture. However, results have been incongruous and the mechanisms of this remain obscured. Therefore, in the current study, carotid plaques were characterized by assessing the levels of MMPs and calcification factors, and evaluating their association with plaque vulnerability. Human carotid plaques were obtained from carotid endarterectomies, and classified into stable and vulnerable groups by ultrasonography and histological analyses. The mRNA and protein levels of MMPs, vascular endothelial growth factor (VEGF), bone sialoprotein 2 (BSP) and osteopontin were investigated by reverse transcription-quantitative polymerase chain reaction and western blotting, respectively. Immunohistochemistry was used to localize MMP-2 and MMP-14 in stable and vulnerable plaques. The activation of various associated signaling pathways was also investigated using western blotting. The mRNA levels of MMP-2, -7, -9 and -14 were elevated in vulnerable plaques, among which expression of MMP-2 and -14 were the highest. Consistent with the mRNA levels, the protein levels of MMP-2 and -14 were also elevated. Immunohistochemistry also demonstrated positive staining of MMP-2 and MMP-14 in vulnerable plaques. Factors that indicate neovascularization and calcification, including VEGF and BSP, were concurrently elevated in vulnerable plaques. In addition, the protein levels of extracellular regulated kinase (ERK) and protein kinase C (PKC) were upregulated in vulnerable plaques. The current study provides novel insights into the MMP profiles of vulnerability plaques, and may assist in the development of novel methods for the diagnosis of plaque vulnerability and the prevention of plaque rupture.

Quantitatively Identifying the Roles of Interfacial Water and Solid Surface in Governing Peptide Adsorption

Understanding the molecular mechanism of protein adsorption on solids is critical to their applications in materials synthesis and tissue engineering. Although the water phase at the surface/water interface has been recognized as three types: bulk water, intermediate water phase and surface-bound water layers, the roles of the water and surface in determining the protein adsorption are not clearly identified, particularly at the quantitative level. Herein, we provide a methodology involving the combination of microsecond strengthen sampling simulation and force integration to quantitatively characterize the water-induced contribution and the peptide-surface interactions into the adsorption free energy. Using hydroxyapatite and graphene surfaces as examples, we demonstrate how the distinct interfacial features dominate the delicate force balance between these two thermodynamics parameters, leading to surface preference/resistance to peptide adsorption. Specifically, the water layer provides sustained repelling force against peptide adsorption, as indicated by a monotonic increase in the water-induced free energy profile, whereas the contribution from the surface-peptide interactions is thermodynamically favorable to peptide adsorptions. More importantly, the revealed adsorption mechanism is critically dictated by the distribution of water phase, which plays a crucial role in establishing the force balance between the interactions of the peptide with the water layer and the surface. For the HAP surface, the charged peptide exhibits strong binding affinity to the surface, due to the controlling contribution of peptide-surface interaction in the intermediate water phase. The surface-bound water layers are observed as the origin of bioresistance of solid surfaces toward the adsorption of charge-neutral peptides. The preferred peptide adsorption on the graphene, however, is dominated by the surface-induced component at the water layers adjacent to the surface. Our results further elucidate that the intermediate water phase significantly shortens the effective range of the surface dispersion force, in contrast to the observation on the hydrophilic surface.

Osteocalcin facilitates calcium phosphate ion complex growth as revealed by free energy calculation

The nanoscopic structural and thermodynamic basis of biomolecule-regulated assembly and crystallization of inorganic solids have a tremendous impact on the rational design of novel functional nanomaterials, but are concealed by many difficulties in molecular-level characterization. Here we demonstrate that the free energy calculation approach, enabled by combining advanced molecular simulation techniques, can unravel the structural and energetic mechanisms of protein-mediated inorganic solid nucleation. It is observed that osteocalcin (OCN), an important non-collagenous protein involved in regulating bone formation, promotes the growth of nanosized calcium phosphate (CaP) ion clusters from a supersaturated solution. Free energy calculation by umbrella sampling indicates that this effect by OCN is prominent at the scale of 1 to 3 nm ion-association complexes (IACs). The binding interactions between gamma-carboxyl glutamate and the C-terminal and, interestingly, the arginine side chains of OCN and IACs stabilize under-coordinated IACs, thus promoting their growth. The promoter effect of OCN on the enlargement and further aggregation of IACs into cluster assemblies of tens of nm are confirmed by conventional molecular dynamics simulation and dynamic light scattering experiments. To the best of our knowledge, this is the first time that the free energy landscape of the early stages of CaP nucleation is shown. The free energy change as a function of IAC size shares the feature of decreasing monotonically as shown previously for the calcium carbonate system. Therefore, the nucleation of both these major biominerals apparently involves an initial phase of liquid-like ionic aggregates. The structural and thermodynamic information regarding OCN-CaP interactions amplifies the current understanding of biomineralization mechanisms at the nanoscale, with general relevance to biomolecule-tuned fabrication of inorganic materials.

Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.

Polypeptide self-assemblies: nanostructures and bioapplications

Polypeptide copolymers can self-assemble into diverse aggregates. The morphology and structure of aggregates can be varied by changing molecular architectures, self-assembling conditions, and introducing secondary components such as polymers and nanoparticles. Polypeptide self-assemblies have gained significant attention because of their potential applications as delivery vehicles for therapeutic payloads and as additives in the biomimetic mineralization of inorganics. This review article provides an overview of recent advances in nanostructures and bioapplications related to polypeptide self-assemblies. We highlight recent contributions to developing strategies for the construction of polypeptide assemblies with increasing complexity and novel functionality that are suitable for bioapplications. The relationship between the structure and properties of the polypeptide aggregates is emphasized. Finally, we briefly outline our perspectives and discuss the challenges in the field.

Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity

Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.

Deciphering Intrinsic Inter-subunit Couplings that Lead to Sequential Hydrolysis of F1-ATPase Ring

Rotary sequential hydrolysis of the metabolic machine F₁-ATPase is a prominent manifestation of high coordination among multiple chemical sites in ring-shaped molecular machines, and it is also functionally essential for F₁ to tightly couple chemical reactions and central γ-shaft rotation. High-speed AFM experiments have identified that sequential hydrolysis is maintained in the F₁ stator ring even in the absence of the γ-rotor. To explore the origins of intrinsic sequential performance, we computationally investigated essential inter-subunit couplings on the hexameric ring of mitochondrial and bacterial F₁. We first reproduced in stochastic Monte Carlo simulations the experimentally determined sequential hydrolysis schemes by kinetically imposing inter-subunit couplings and following subsequent tri-site ATP hydrolysis cycles on the F₁ ring. We found that the key couplings to support the sequential hydrolysis are those that accelerate neighbor-site ADP and Pi release upon a certain ATP binding or hydrolysis reaction. The kinetically identified couplings were then examined in atomistic molecular dynamics simulations at a coarse-grained level to reveal the underlying structural mechanisms. To do that, we enforced targeted conformational changes of ATP binding or hydrolysis to one chemical site on the F₁ ring and monitored the ensuing conformational responses of the neighboring sites using structure-based simulations. Notably, we found asymmetrical neighbor-site opening that facilitates ADP release upon enforced ATP binding. We also captured a complete charge-hopping process of the Pi release subsequent to enforced ATP hydrolysis in the neighbor site, confirming recent single-molecule analyses with regard to the role of ATP hydrolysis in F₁. Our studies therefore elucidate both the coordinated chemical kinetics and structural dynamics mechanisms underpinning the sequential operation of the F₁ ring.

Effects of atomic-level nano-structured hydroxyapatite on adsorption of bone morphogenetic protein-7 and its derived peptide by computer simulation

Hydroxyapatite (HA) is the principal inorganic component of bones and teeth and has been widely used as a bone repair material because of its good biocompatibility and bioactivity. Understanding the interactions between proteins and HA is crucial for designing biomaterials for bone regeneration. In this study, we evaluated the effects of atomic-level nano-structured HA (110) surfaces on the adsorption of bone morphogenetic protein-7 (BMP-7) and its derived peptide (KQLNALSVLYFDD) using molecular dynamics and density functional theory methods. The results indicated that the atomic-level morphology of HA significantly affected the interaction strength between proteins and HA substrates. The interactions of BMP-7 and its derived peptide with nano-concave and nano-pillar HA surfaces were stronger than those with flat or nano-groove HA surfaces. The results also revealed that if the groove size of nano-structured HA surfaces matched that of residues in the protein or peptide, these residues were likely to spread into the grooves of the nano-groove, nano-concave, and nano-pillar HA, further strengthening the interactions. These results are helpful in better understanding the adsorption behaviors of proteins onto nano-structured HA surfaces, and provide theoretical guidance for designing novel bioceramic materials for bone regeneration and tissue engineering.

On the surface effects of citrates on nano-apatites: evidence of a decreased hydrophilicity

The surface structure and hydrophilicity of synthetic nanocrystalline apatite with strongly bound citrates on their surface are here investigated at the molecular level, by combining advanced IR spectroscopy, microgravimetry and adsorption microcalorimetry. Citrate are found to form unidentate-like and ionic-like complexes with surface Ca²⁺ ions, with a surface coverage closely resembling that present in bone apatite platelets (i.e., 1 molecule/(n nm)², with n ranging between 1.4 and 1.6). These surface complexes are part of a hydrated non-apatitic surface layer with a sub-nanometre thickness. Noticeably, it is found that the hydrophilicity of the nanoparticles, measured in terms of adsorption of water molecules in the form of multilayers, decreases in a significant extent in relation to the presence of citrates, most likely because of the exposure toward the exterior of –CH₂ groups. Our findings provide new insights on the surface properties of bio-inspired nano-apatites, which can be of great relevance for better understanding the role of citrate in determining important interfacial properties, such as hydrophobicity, of bone apatite platelets. The evaluation and comprehension of surface composition and structure is also of paramount interest to strictly control the functions of synthetic biomaterials, since their surface chemistry strongly affects the hosting tissue response.

Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides

Dentin phosphoprotein (DPP) is the most acidic protein in vertebrates and structurally is classified as an intrinsically disordered protein. Functionally, DPP is related to dentin and bone formation, however the specifics of such association remain unknown. Here, we used atomistic molecular dynamics simulations to screen selected binding domains of DPP onto hydroxyapatite (HA), which is one of its important interacting partners. From these results, we selected a functionally relevant peptide, Ace-SSDSSDSSDSSDSSD-NH2 (named P5) and its phosphorylated form (named P5P), for experimental characterization. SAXS experiments indicated that in solution P5 was disordered, possibly in an extended conformation while P5P displayed more compact globular conformations. Circular dichroism and FTIR confirmed that, either in the presence or absence of Ca2+/HA, P5 adopts a random coil structure, whereas its phosphorylated counterpart, P5P, has a more compact arrangement associated with conformations that display β-sheet and α-helix motifs when bound to HA. In solution, P5 inhibited HA crystal growth, whereas at similar concentrations, P5P stimulated it. These findings suggest that phosphorylation controls the transient formation of secondary and tertiary structure of DPP peptides, and, most likely of DPP itself, which in turn controls HA growth in solution and possibly HA growth in mineralized tissues.

The Role of AGE/RAGE Signaling in Diabetes-Mediated Vascular Calcification

AGE/RAGE signaling has been a well-studied cascade in many different disease states, particularly diabetes. Due to the complex nature of the receptor and multiple intersecting pathways, the AGE/RAGE signaling mechanism is still not well understood. The purpose of this review is to highlight key areas of AGE/RAGE mediated vascular calcification as a complication of diabetes. AGE/RAGE signaling heavily influences both cellular and systemic responses to increase bone matrix proteins through PKC, p38 MAPK, fetuin-A, TGF-β, NFκB, and ERK1/2 signaling pathways in both hyperglycemic and calcification conditions. AGE/RAGE signaling has been shown to increase oxidative stress to promote diabetes-mediated vascular calcification through activation of Nox-1 and decreased expression of SOD-1. AGE/RAGE signaling in diabetes-mediated vascular calcification was also attributed to increased oxidative stress resulting in the phenotypic switch of VSMCs to osteoblast-like cells in AGEs-induced calcification. Researchers found that pharmacological agents and certain antioxidants decreased the level of calcium deposition in AGEs-induced diabetes-mediated vascular calcification. By understanding the role the AGE/RAGE signaling cascade plays diabetes-mediated vascular calcification will allow for pharmacological intervention to decrease the severity of this diabetic complication.

Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation

Understanding the molecular structural and energetic basis of the interactions between peptides and inorganic surfaces is critical to their applications in tissue engineering and biomimetic material synthesis. Despite recent experimental progresses in the identification and functionalization of hydroxyapatite (HAP)-binding peptides, the molecular mechanisms of their interactions with HAP surfaces are yet to be explored. In particular, the traditional method of molecular dynamics (MD) simulation suffers from insufficient sampling at the peptide-inorganic interface that renders the molecular-level observation dubious. Here we demonstrate that an integrated approach combining bioinformatics, MD, and metadynamics provides a powerful tool for investigating the structure-activity relationship of HAP-binding peptides. Four low charge density peptides, previously identified by phage display, have been considered. As revealed by bioinformatics and MD, the binding conformation of the peptides is controlled by both the sequence and the amino acid composition. It was found that formation of hydrogen bonds between lysine residue and phosphate ions on the surface dictates the binding of positively charged peptide to HAP. The binding affinities of the peptides to the surface are estimated by free energy calculation using parallel-tempering metadynamics, and the results compare favorably to measurements reported in previous experimental studies. The calculation suggests that the charge density of the peptide primarily controls the binding affinity to the surface, while the backbone secondary structure that may restrain side chain orientation toward the surface plays a minor role. We also report that the application of enhanced-sampling metadynamics effects a major advantage over the steered MD method by significantly improving the reliability of binding free energy calculation. In general, our novel integration of diverse sampling techniques should contribute to the rational design of surface-recognition peptides in biomedical applications.

Surface Functionalization of Orthopedic Titanium Implants with Bone Sialoprotein

Orthopedic implant failure due to aseptic loosening and mechanical instability remains a major problem in total joint replacement. Improving osseointegration at the bone-implant interface may reduce micromotion and loosening. Bone sialoprotein (BSP) has been shown to enhance bone formation when coated onto titanium femoral implants and in rat calvarial defect models. However, the most appropriate method of BSP coating, the necessary level of BSP coating, and the effect of BSP coating on cell behavior remain largely unknown. In this study, BSP was covalently coupled to titanium surfaces via an aminosilane linker (APTES), and its properties were compared to BSP applied to titanium via physisorption and untreated titanium. Cell functions were examined using primary human osteoblasts (hOBs) and L929 mouse fibroblasts. Gene expression of specific bone turnover markers at the RNA level was detected at different intervals. Cell adhesion to titanium surfaces treated with BSP via physisorption was not significantly different from that of untreated titanium at any time point, whereas BSP application via covalent coupling caused reduced cell adhesion during the first few hours in culture. Cell migration was increased on titanium disks that were treated with higher concentrations of BSP solution, independent of the coating method. During the early phases of hOB proliferation, a suppressive effect of BSP was observed independent of its concentration, particularly when BSP was applied to the titanium surface via physisorption. Although alkaline phosphatase activity was reduced in the BSP-coated titanium groups after 4 days in culture, increased calcium deposition was observed after 21 days. In particular, the gene expression level of RUNX2 was upregulated by BSP. The increase in calcium deposition and the stimulation of cell differentiation induced by BSP highlight its potential as a surface modifier that could enhance the osseointegration of orthopedic implants. Both physisorption and covalent coupling of BSP are similarly effective, feasible methods, although a higher BSP concentration is recommended.

Intrinsically disordered proteins and biomineralization

In vertebrates and invertebrates, biomineralization is controlled by the cell and the proteins they produce. A large number of these proteins are intrinsically disordered, gaining some secondary structure when they interact with their binding partners. These partners include the component ions of the mineral being deposited, the crystals themselves, the template on which the initial crystals form, and other intrinsically disordered proteins and peptides. This review speculates why intrinsically disordered proteins are so important for biomineralization, providing illustrations from the SIBLING (small integrin binding N-glycosylated) proteins and their peptides. It is concluded that the flexible structure, and the ability of the intrinsically disordered proteins to bind to a multitude of surfaces is crucial, but details on the precise-interactions, energetics and kinetics of binding remain to be determined.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Molecular mechanics of the cooperative adsorption of a Pro-Hyp-Gly tripeptide on a hydroxylated rutile TiO2(110) surface mediated by calcium ions

Calcium ions play an cooperative role during peptide adsorption on the hydroxylated rutile TiO₂(110) surface and the molecular mechanics was studied.

Differences in the calcification of preosteoblast cultured on sputter-deposited titanium, zirconium, and gold

In this study, osteogenic differentiation and calcification of preosteoblast (MC3T3-E1) cultured on sputter-deposited titanium (Ti), zirconium (Zr), and gold (Au) on cover glasses were evaluated to understand the differences in bone formation ability among these three metals; these metals show the same high corrosion resistance, but Ti and Zr are covered by surface passive oxide film while Au is not covered by the oxide film. Ti and Zr promoted cellular proliferation without osteogenic differentiation. Cells cultured on Ti and Zr expressed higher levels of Runx2, Col1α1, and Akp2 at an earlier stage, which indicated faster promotion of osteogenic differentiation, as compared to those cultured on Au. Moreover, after 21 days of culture, the Bglap1 and Ifitm5 expression peaks in cells cultured on Ti and Zr were higher than those in cells cultured on Au, which indicated faster promotion of calcification. Cells cultured on Ti showed an advantage in osteogenic differentiation at an early stage, while cells on Zr showed better calcification promotion with a long-term culture. The amount of extracellular calcified deposits was in good agreement with the gene expression results. On the other hand, the intracellular calcium content of cells on Au specimens was higher than that of cells on Ti and Zr specimens. The results indicate that preosteoblasts on Ti and Zr showed faster osteogenic differentiation and calcification than those on Au, whereas Au improved the intracellular calcium content. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 639-651, 2016.

A potential mechanism for amino acid-controlled crystal growth of hydroxyapatite

The mineral component of bone, dentin and calcified parts of avian tendon, hydroxyapatite (HAP), has non-stoichiometric composition (idealized as Ca₁₀(PO₄)₆(OH)₂), plate-like morphology and nanometer size. This unique crystal morphology contributes to the physico-chemical and biochemical properties of bone. Thus, understanding the mechanism for the controlled growth of plate-like HAP nanocrystals is significant in the study of bone biomineralization. Previous studies have shown that acidic non-collagenous proteins (ANCPs), which are enriched in the residues of acidic amino acids, may play an important role in HAP crystal growth modulation. In this study, glutamic acid (Glu) and phosphoserine (Ser-OPO₃) were used as model compounds to modify the synthesis of HAP nanocrystals. To identify the mechanisms of amino acids as regulators, X-ray diffraction (XRD), transmission electron microscopy (TEM) and solid state nuclear magnetic resonance (ssNMR) were used. The crystals obtained in the inorganic controls were needle-like, while crystals synthesized in the presence of the amino acids presented a plate-like morphology. The plate-like crystals had a preferred crystal orientation on (300) face, which was lacking in the inorganically grown crystals, indicating preferential adsorption and suppression of growth in specific crystal directions. Ser-OPO₃ was more efficient than Glu in modulating HAP nucleation and crystal growth. Furthermore, NMR revealed interactions between the charged side chain groups in amino acids and the crystal surfaces. These results were successfully explained through our MD simulations for the free energy calculation of amino acid binding on HAP crystal faces. The present study revealed that amino acids may act as effective regulators of HAP morphology without the need to invoke large NCPs in bone biomineralization and in designing bioinspired materials for orthopaedic and dental applications.

Oxidized low-density lipoprotein increases bone sialoprotein expression in vascular smooth muscle cells via runt-related transcription factor 2

BACKGROUND

Vascular calcification is a pivotal stage in atherosclerosis. During vascular calcification, vascular smooth muscle cells (VSMCs) synthesize many osteogenic factors such as bone sialoprotein (BSP). Oxidative stress plays a critical role in progression of atherosclerosis and also increases extracellular matrix proteins expression. BSP overexpression has been observed during vascular calcification by oxidative stress. However, the regulatory mechanism of oxidized low-density lipoprotein (oxLDL)-mediated vascular calcification has not yet been fully defined. In this study, we aimed to investigate whether runt-related transcription factor 2 (Runx2) affects the oxLDL-induced BSP expression or not.

METHODS

In this experimental study, we cultured VSMCs in F12K media and then treated them with oxLDL. The expression of Runx2 and BSP genes was determined by real-time polymerase chain reaction method. Protein level of each gene was investigated by Western blotting technique. To determine whether Runx2 regulates BSP gene expression at VSMCs induced by oxLDL, we suppressed Runx2 mRNA using siRNA. Transfected cells then were treated with oxLDL and expression of Runx2 and BSP genes was determined again.

RESULTS

oxLDL increased Runx2 and BSP expression (4.8 ± 0.47-fold and 4.91 ± 0.56-fold, respectively) after 48 hours. Western blotting method confirmed the increased levels of Runx2 and BSP proteins after 48 hours. Runx2 overexpression alone induced BSP expression, whereas knockdown of Runx2 with small interfering siRNA blocked oxLDL-induced BSP expression.

CONCLUSIONS

Our results showed that oxLDL-induced BSP expression was dependent on Runx2 expression, suggesting that Runx2 is required for oxLDL-induced BSP expression.

Organized intrafibrillar mineralization, directed by a rationally designed multi-functional protein

Taking lessons from the structure-forming process of biominerals in animals and plants, one can find tremendous inspirations and ideas for developing advanced synthesis techniques, which is called bio-process inspired synthesis. Bone, as a typical representative of biominerals, is constituted of mineralized collagen fibrils, which are formed under the functions of non-collagenous proteins (NCPs). Intrafibrillar mineralization is the consequence of a synergy among several NCPs. In the present study, we have designed a multi-functional protein, named (MBP)-BSP-HAP, based on bone sialoprotein (BSP) and hydroxyapatite binding protein (HAP), to mimic the intrafibrillar mineralization process in vitro. The three functional domains of (MBP)-BSP-HAP provide the artificial protein with multiple designated functions for intrafibrillar mineralization including binding calcium ions, binding collagen, and binding hydroxyapatite. Platelet-like hydroxyapatite crystals periodically arranged inside the collagen fibrils have been achieved under the function of (MBP)-BSP-HAP. The mechanism of intrafibrillar mineralization directed by the multi-functional protein was proposed. This work may not only shed light on bio-process inspired approaches for more economic and efficient biomimetic synthesis, but also be helpful in understanding the natural process of bone formation for bone regeneration and tissue repair.

Human recombinant cementum attachment protein (hrPTPLa/CAP) promotes hydroxyapatite crystal formation in vitro and bone healing in vivo

Cementum extracellular matrix is similar to other mineralized tissues; however, this unique tissue contains molecules only present in cementum. A cDNA of these molecules, cementum attachment protein (hrPTPLa/CAP) was cloned and expressed in a prokaryotic system. This molecule is an alternative splicing of protein tyrosine phosphatase-like A (PTPLa). In this study, we wanted to determine the structural and functional characteristics of this protein. Our results indicate that hrPTPLa/CAP contains a 43.2% α-helix, 8.9% β-sheet, 2% β-turn and 45.9% random coil secondary structure. Dynamic light scattering shows that this molecule has a size distribution of 4.8 nm and aggregates as an estimated mass of 137 kDa species. AFM characterization and FE-SEM studies indicate that this protein self-assembles into nanospheres with sizes ranging from 7.0 to 27 nm in diameter. Functional studies demonstrate that hrPTPLa/CAP promotes hydroxyapatite crystal nucleation: EDS analysis revealed that hrPTPLa/CAP-induced crystals had a 1.59 ± 0.06 Ca/P ratio. Further confirmation with MicroRaman spectrometry and TEM confirm the presence of hydroxyapatite. In vivo studies using critical-size defects in rat cranium showed that hrPTPLa/CAP promoted 73% ± 2.19% and 87% ± 1.97% new bone formation at 4 and 8 weeks respectively. Although originally identified in cementum, PTPLa/CAP is very effective at inducing bone repair and healing and therefore this novel molecule has a great potential to be used for mineralized tissue bioengineering and tissue regeneration.

Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues

The critical role of the self-assembled structure of collagen in skeletal mineralization is long recognized, yet the angstrom to tens of nanometers length-scale nucleation mechanism of calcium phosphate mineral (Ca-Pi) remains unclear. Here, by constructing three-dimensional structure of collagen fibril, we report direct computational evidence of intrafibrillar Ca-Pi nucleation in the collagen matrix and illustrate the crucial role of charged amino acid sidechains of collagen molecules in nucleation. The all-atom Hamiltonian replica exchange molecular dynamics simulation shows that these charged sidechains are oriented toward the fibril "hole zones" and significantly template nucleation with amorphous Ca-Pi phase, ∼1.3-1.6 nm in size, thus explaining the empirical observations that Ca-Pi nucleates principally in these regions. We also show that the low water density of about 0.70 g cm(-3) in these zones may further benefit nucleation by lowering the enthalpic penalty for ion desolvation. This work provides insight, at the atomistic level, into the nucleation mechanism of bone crystals within a collagen matrix for understanding mineral deposition, interpreting mineralization experiments and guiding the design of new implantable materials.

The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution--accurate computational models and experiment

Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1-1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed.