Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces

Enhanced bone morphogenic property of parylene-C

The ability to induce osteointegration was introduced to a parylene-C surface via the simple and intuitive process of protein adsorption mediated by hydrophobic interactions. In this way, bone morphogenetic protein (BMP)-2, fibronectin, and platelet-rich plasma (PRP) could be immobilized on parylene-C surfaces. This approach alleviates concerns related to the use of potentially harmful substances in parylene-C modification processes. The adsorbed protein molecules were quantitatively characterized with respect to adsorption efficacy and binding affinity, and the important biological activities of the proteins were also examined using both early and late markers of osteogenetic activity, including alkaline phosphatase expression, calcium mineralization and marker gene expression. Additionally, the adsorbed PRP exhibited potential as a substitute for expensive recombinant growth factors by effectively inducing comparable osteogenetic activity. In addition to the excellent biocompatibility of parylene-C and its ability to coat a wide variety of substrate materials, the modification of parylene-C via protein adsorption provides unlimited possibilities for installing specific biological functions, expanding the potential applications of this material to include various biointerface platforms.

Hierarchical structures on nickel-titanium fabricated by ultrasonic nanocrystal surface modification

Hierarchical structures on metallic implants can enhance the interaction between cells and implants and thus increase their biocompatibility. However, it is difficult to directly fabricate hierarchical structures on metallic implants. In this study, we used a simple one-step method, ultrasonic nanocrystal surface modification (UNSM), to fabricate hierarchical surface structures on a nickel-titanium (NiTi) alloy. During UNSM, a tungsten carbide ball hits metal surfaces at ultrasonic frequency. The overlapping of the ultrasonic strikes generates hierarchical structures with microscale grooves and embedded nanoscale wrinkles. Cell culture experiments showed that cells adhere better and grow more prolifically on the UNSM-treated samples. Compared with the untreated samples, the UNSM-treated samples have higher corrosion resistance. In addition, the surface hardness increased from 243 Hv to 296 Hv and the scratch hardness increased by 22%. Overall, the improved biocompatibility, higher corrosion resistance, and enhanced mechanical properties demonstrate that UNSM is a simple and effective method to process metallic implant 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.

Probing the surface structure of hydroxyapatite through its interaction with hydroxyl: a first-principles study

Understanding the interaction of the hydroxyapatite (HAp) surface with hydroxyl originating from either the alkalescent physiological environment or HAp itself is crucial for the development of HAp-based biomaterials. Periodical density functional theory calculations were carried out in this study to explore the interaction of the HAp (100), (010) and (001) facets with hydroxyl. Based on a comparison study of Ca-rich, PO4-rich and Ca-PO4-OH mixed surfaces, the interaction pattern, interaction energy and effect of an additional water molecule on the Ca-OH interaction were comprehensively studied. The formation of CaOH on the Ca-rich surface was energetically favored on (100) and (001), while Ca(OH)2 was energetically favored on (010). The Ca-water interaction was competitive, but had lower interaction energy than Ca-OH. Furthermore, Ca-O bonding and its influence on the OH stretching vibration were analyzed. Our calculations suggest that the hydroxyl-coated surface structure is more appropriate than the commonly used Ca-terminated surface model for studying HAp surface activity in its service environments.

Theoretical studies on key factors in DNA sequencing using atomically thin molybdenum disulfide nanopores

Applied voltage and MoS₂ nanopore diameter affect the resolution of MoS₂ nanopore-based DNA sequencing.

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.

Adsorption Behavior and Mechanism of SCA-1 on a Calcite Surface: A Molecular Dynamics Study

The crystallization mechanism for natural mineral, especially the role of biological molecules in biomineralization, is still under debate. Protein adsorption on material surfaces plays a key role in biomineralization. In this article, molecular dynamics (MD) simulations were performed to systematically investigate the adsorption behavior of struthio camelus eggshell protein struthiocalcin-1 (SCA-1) on the calcite (104) surface with several different starting orientations in an explicit water environment. For each binding configuration, detailed adsorption behaviors and a mechanism were presented with the analysis of interaction energy, binding residues, hydrogen bonding, and structures (such as DSSP, dipole moment, and the electrostatic potential calculation). The results indicate that the positively charged and polar residues are the dominant residues for protein adsorption on the calcite (104) surface, and the strong electrostatic interaction drives the binding of model protein to the surface. The hydrogen bond bridge was found to play an important role in surface interactions as well. These results also demonstrate that SCA-1 is relatively rigid in spite of strong adsorption with few structural changes in α-helix and β-sheet contents. The results of the orientation calculation suggest that the dipole moment of the protein tends to remain parallel to calcite in most stable cases, which was confirmed by electrostatic potential isosurfaces analysis.

Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation. As a means to circumvent these problems, the authors demonstrate the application of an efficient advanced sampling method (TIGER2A) for the simulation of the adsorption of hen egg-white lysozyme on a crystalline (110) high-density polyethylene surface plane. Simulations are conducted to generate a Boltzmann-weighted ensemble of sampled states using force field parameters that were validated to represent interfacial behavior for this system. The resulting ensembles of sampled states were then analyzed using an in-house-developed cluster analysis method to predict the most probable orientations and conformations of the protein on the surface based on the amount of sampling performed, from which free energy differences between the adsorbed states were able to be calculated. In addition, by conducting two independent sets of TIGER2A simulations combined with cluster analyses, the authors demonstrate a method to estimate the degree of convergence achieved for a given amount of sampling. The results from these simulations demonstrate that these methods enable the most probable orientations and conformations of an adsorbed protein to be predicted and that the use of our validated interfacial force field parameter set provides closer agreement to available experimental results compared to using standard CHARMM force field parameterization to represent molecular behavior at the interface.

Surface hydroxyl groups regulate the osteogenic differentiation of mesenchymal stem cells on titanium and tantalum metals

Titanium (Ti) and tantalum (Ta) metals have been widely used as implants for their favorable mechanical features and good biocompatibility. However, the results on their osteogenic capacity have been conflicting due to the synergistic effects of complex and multiple material surface features (such as topography, surface chemistries etc.) on cellular behaviors. Here, we directly compare the osteogenic response of mesenchymal stem cells (MSCs) to Ti and Ta metal surfaces with alterable surface hydroxyl groups. Although no difference was found on both surface topographies, cellular adhesion, proliferation, and the expression of osteogenic-related markers were upregulated with the increasing amount of surface hydroxyl groups (-OH) after ultraviolet (UV) light treatment. Moreover, Ti showed better effects in promoting osteogenic differentiation of MSCs than Ta before UV light treatment, but demonstrated the opposite after UV light treatment. These results might be attributed to the comparative quantity of the distinct type of surface hydroxyl groups (bridging-OH and terminal-OH), which regulated the conformation of the initial protein adsorption and subsequent cellular behaviors. Our results demonstrate the central role of the surface hydroxyl groups in mediating cell-material interactions and implicate this interface as helping in optimizing osteointegration of Ti and Ta based orthopaedic and dental implants.

Enhanced osteogenic activity of anatase TiO2 film: Surface hydroxyl groups induce conformational changes in fibronectin

In this study, with an attempt to identify the effects of TiO₂ crystalline phase compositions on the osteogenic properties, the anatase and rutile TiO₂ thin films with similar film thickness, surface topography and hydrophilicity were prepared on Si (100) substrates by atomic layer deposition (ALD), subsequent thermal annealing and ultraviolet irradiation. The films were studied with XRD, XPS, FE-SEM, AFM, FTIR and contact angle measurements. In vitro cellular assays showed that the anatase phase led to better osteoblast compatibility in terms of adhesion, proliferation, differentiation, mineralization as well as osteogenesis-related gene expression when compared with the rutile phase. We investigated the difference between the anatase and rutile TiO₂ films at the biomolecular level to explain the enhanced osteogenic activity of the anatase film. It was found that the presence of more TiOH groups on anatase surface induced more cell-binding sites of fibronectin (FN) exposed on its surface, causing a more active conformation of the adsorbed FN for subsequent osteoblast behaviors.

Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations

Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS)₅ peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 k_BT per leucine. In good agreement, simulations indicate a similar trend with 2.1 k_BT per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

Cells Recognize and Prefer Bone-like Hydroxyapatite: Biochemical Understanding of Ultrathin Mineral Platelets in Bone

Hydroxyapatite (HAP) nanocrystallites in all types of bones are distinguished by their ultrathin characteristics, which are uniaxially oriented with fibrillar collagen to uniquely expose the (100) faces. We speculate that living organisms prefer the specific crystal morphology and orientation of HAP because of the interactions between cells and crystals at the mineral-cell interface. Here, bone-like platy HAP (p-HAP) and two different rod-like HAPs were synthesized to investigate the ultrathin mineral modulating effect on cell bioactivity and bone generation. Cell viability and osteogenic differentiation of mesenchymal stem cells (MSCs) were significantly promoted by the platy HAP with (100) faces compared to rod-like HAPs with (001) faces as the dominant crystal orientation, which indicated that MSCs can recognize the crystal face and prefer the (100) HAP faces. This face-specific preference is dependent on the selective adsorption of fibronectin (FN), a plasma protein that plays a central role in cell adhesion, on the HAP surface. This selective adsorption is further confirmed by molecule dynamics (MD) simulation. Our results demonstrate that it is an intelligent choice for cells to use ultrathin HAP with a large (100) face as a basic building block in the hierarchical structure of bone, which is crucial to the promotion of MSCs osteoinductions during bone formation.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Accelerated Molecular Dynamics Study of the Effects of Surface Hydrophilicity on Protein Adsorption

The adsorption of streptavidin is studied on two surfaces, graphite and titanium dioxide, using accelerated molecular dynamics. Adsorption on graphite leads to strong conformational changes while the protein spreads out over the surface. Interestingly, also adsorption on the highly hydrophilic rutile surface induces considerable spreading of the protein. We pin down the cause for this unfolding to the interaction of the protein with the ordered water layers above the rutile surface. For special orientations, the protein penetrates the ordered water layers and comes into direct contact with the surface where the positively charged amino acids settle in places adjacent to the negatively charged top surface atom layer of rutile. We conclude that for both surface materials studied, streptavidin changes its conformation so strongly that it loses its potential for binding biotin. Our results are in good qualitative agreement with available experimental studies.

Forced Desorption of Bovine Serum Albumin and Lysozyme from Graphite: Insights from Molecular Dynamics Simulation

We use molecular dynamics (MD) simulation to study the adsorption and desorption of two widely different proteins, bovine serum albumin (BSA) and lysozyme, on a graphite surface. The adsorption is modeled using accelerated MD to allow the proteins to find optimum conformations on the surface. Our results demonstrate that the "hard protein" lysozyme retains much of its secondary structure during adsorption, whereas BSA loses it almost completely. BSA has a considerably larger adsorption energy compared to that of lysozyme, which does not scale with chain length. Desorption simulations are carried out using classical steered MD. The BSA molecule becomes fully unzipped during pull-off, whereas several helices survive this process in lysozyme. The unzipping process shows up in the force-distance curve of BSA as a series of peaks, whereas only a single or few, depending on protein orientation, force peaks occur for lysozyme. The maximum desorption force is larger for BSA than for lysozyme, but only by a factor of about 2.3.

The Process of Separating Bovine Serum Albumin Using Hydroxyapatite and Active Babassu Coal (Orbignya martiana)

Bovine serum albumin is one of the major serum proteins; it plays an important role as a result of its functional and nutritional properties which have bioactive peptides. Adsorption method was used to separate protein, which involves hydroxyapatite, synthetic hydroxyapatite, and active babassu coal. Initially, characterization was carried out using the zeta potential of the adsorbents. Kinetic pseudo-first- and pseudo-second-order models were applied. For isotherms, equilibrium data studies were carried out using the Langmuir and Freundlich models, in addition to determining the efficiency of adsorptive process. The results of the zeta potential showed loads ranging from +6.9 to -42.8 mV. The kinetic data were better represented in the pseudo-second-order model with chemisorption characteristics. The adsorption capacity of the adsorbents decreased as pH increased, indicating that the electrostatic bonds and some functional groups of active babassu coal contributed to the reduction of adsorption, especially oxygen linked to carbon atoms. The value of pH 4.0 showed the best results of adsorption, being obtained as the maximum adsorption capacity (q m ) and yield (%) (where q m = 87.95 mg g(-1) and 74.2%; 68.26 mg g(-1) and 68.6%; and 36.18 mg g(-1), 37.4%) of hydroxyapatite, synthetic hydroxyapatite, and active babassu coal, respectively.

Strong Electrostatic Interactions Lead to Entropically Favorable Binding of Peptides to Charged Surfaces

Thermodynamic analyses can provide key insights into the origins of protein self-assembly on surfaces, protein function, and protein stability. However, obtaining quantitative measurements of thermodynamic observables from unbiased classical simulations of peptide or protein adsorption is challenging because of sampling limitations brought on by strong biomolecule/surface binding forces as well as time scale limitations. We used the parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) enhanced sampling method to study the adsorption behavior and thermodynamics of several explicitly solvated model peptide adsorption systems, providing new molecular-level insight into the biomolecule adsorption process. Specifically studied were peptides LKα14 and LKβ15 and trpcage miniprotein adsorbing onto a charged, hydrophilic self-assembled monolayer surface functionalized with a carboxylic acid/carboxylate headgroup and a neutral, hydrophobic methyl-terminated self-assembled monolayer surface. Binding free energies were calculated as a function of temperature for each system and decomposed into their respective energetic and entropic contributions. We investigated how specific interfacial features such as peptide/surface electrostatic interactions and surface-bound ion content affect the thermodynamic landscape of adsorption and lead to differences in surface-bound conformations of the peptides. Results show that upon adsorption to the charged surface, configurational entropy gains of the released solvent molecules dominate the configurational entropy losses of the bound peptide. This behavior leads to an apparent increase in overall system entropy upon binding and therefore to the surprising and seemingly nonphysical result of an apparent increased binding free energy at elevated temperatures. Opposite effects and conclusions are found for the neutral surface. Additional simulations demonstrate that by adjusting the ionic strength of the solution, results that show the expected physical behavior, i.e., peptide binding strength that decreases with increasing temperature or is independent of temperature altogether, can be recovered on the charged surface. On the basis of this analysis, an overall free energy for the entire thermodynamic cycle for peptide adsorption on charged surfaces is constructed and validated with independent simulations.

Adverse Biological Effect of TiO₂ and Hydroxyapatite Nanoparticles Used in Bone Repair and Replacement

The adverse biological effect of nanoparticles is an unavoidable scientific problem because of their small size and high surface activity. In this review, we focus on nano-hydroxyapatite and TiO₂ nanoparticles (NPs) to clarify the potential systemic toxicological effect and cytotoxic response of wear nanoparticles because they are attractive materials for bone implants and are widely investigated to promote the repair and reconstruction of bone. The wear nanoparticles would be prone to binding with proteins to form protein-particle complexes, to interacting with visible components in the blood including erythrocytes, leukocytes, and platelets, and to being phagocytosed by macrophages or fibroblasts to deposit in the local tissue, leading to the formation of fibrous local pseudocapsules. These particles would also be translocated to and disseminated into the main organs such as the lung, liver and spleen via blood circulation. The inflammatory response, oxidative stress, and signaling pathway are elaborated to analyze the potential toxicological mechanism. Inhibition of the oxidative stress response and signaling transduction may be a new therapeutic strategy for wear debris-mediated osteolysis. Developing biomimetic materials with better biocompatibility is our goal for orthopedic implants.

Surface Structure of Hydroxyapatite from Simulated Annealing Molecular Dynamics Simulations

The surface structure of hydroxyapatite (HAP) is crucial for its bioactivity. Using a molecular dynamics simulated annealing method, we studied the structure and its variation with annealing temperature of the HAP (100) surface. In contrast to the commonly used HAP surface model, which is sliced from HAP crystal and then relaxed at 0 K with first-principles or force-field calculations, a new surface structure with gradual changes from ordered inside to disordered on the surface was revealed. The disordering is dependent on the annealing temperature, Tmax. When Tmax increases up to the melting point, which was usually adopted in experiments, the disordering increases, as reflected by its radial distribution functions, structural factors, and atomic coordination numbers. The disordering of annealed structures does not show significant changes when Tmax is above the melting point. The thickness of disordered layers is about 10 Å. The surface energy of the annealed structures at high temperature is significantly less than that of the crystal structure relaxed at room temperature. A three-layer model of interior, middle, and surface was then proposed to describe the surface structure of HAP. The interior layer retains the atomic configurations in crystal. The middle layer has its atoms moved and its groups rotated about their original locations. In the surface layer, the atomic arrangements are totally different from those in crystal. In particular for the hydroxyl groups, they move outward and cover the Ca(2+) ions, leaving holes occupied by the phosphate groups. Our study suggested a new model with disordered surface structures for studying the interaction of HAP-based biomaterials with other molecules.

Magnesium modification up-regulates the bioactivity of bone morphogenetic protein-2 upon calcium phosphate cement via enhanced BMP receptor recognition and Smad signaling pathway

Efficient presentation of growth factors is one of the great challenges in tissue engineering. In living systems, bioactive factors exist in soluble as well as in matrix-bound forms, both of which play an integral role in regulating cell behaviors. Herein, effect of magnesium on osteogenic bioactivity of recombinant human bone morphogenetic protein-2 (rhBMP-2) was investigated systematically with a series of Mg modified calcium phosphate cements (xMCPCs, x means the content of magnesium phosphate cement wt%) as matrix model. The results indicated that the MCPC, especially 5MCPC, could promote the rhBMP-2-induced in vitro osteogenic differentiation via Smad signaling of C2C12 cells. Further studies demonstrated that all MCPC substrates exhibited similar rhBMP-2 release rate and preserved comparable conformation and biological activity of the released rhBMP-2. Also, the ionic extracts of MCPC made little difference to the bioactivity of rhBMP-2, either in soluble or in matrix-bound forms. However, with the quartz crystal microbalance (QCM), we observed a noticeable enhancement of rhBMP-2 mass-uptake on 5MCPC as well as a better recognition of the bound rhBMP-2 to BMPR IA and BMPR II. In vivo results demonstrated a better bone regeneration capacity of 5MCPC/rhBMP-2. From the above, our results demonstrated that it was the Mg anchored on the underlying substrates that tailored the way of rhBMP-2 bound on MCPC, and thus facilitated the recognition of BMPRs to stimulate osteogenic differentiation. The study will guide the development of Mg-doped bioactive bone implants for tissue regeneration.

Facilitated receptor-recognition and enhanced bioactivity of bone morphogenetic protein-2 on magnesium-substituted hydroxyapatite surface

Biomaterial surface functionalized with bone morphogenetic protein-2 (BMP-2) is a promising approach to fabricating successful orthopedic implants/scaffolds. However, the bioactivity of BMP-2 on material surfaces is still far from satisfactory and the mechanism of related protein-surface interaction remains elusive. Based on the most widely used bone-implants/scaffolds material, hydroxyapatite (HAP), we developed a matrix of magnesium-substituted HAP (Mg-HAP, 2.2 at% substitution) to address these issues. Further, we investigated the adsorption dynamics, BMPRs-recruitment, and bioactivity of recombinant human BMP-2 (rhBMP-2) on the HAP and Mg-HAP surfaces. To elucidate the mechanism, molecular dynamic simulations were performed to calculate the preferred orientations, conformation changes, and cysteine-knot stabilities of adsorbed BMP-2 molecules. The results showed that rhBMP-2 on the Mg-HAP surface exhibited greater bioactivity, evidenced by more facilitated BMPRs-recognition and higher ALP activity than on the HAP surface. Moreover, molecular simulations indicated that BMP-2 favoured distinct side-on orientations on the HAP and Mg-HAP surfaces. Intriguingly, BMP-2 on the Mg-HAP surface largely preserved the active protein structure evidenced by more stable cysteine-knots than on the HAP surface. These findings explicitly clarify the mechanism of BMP-2-HAP/Mg-HAP interactions and highlight the promising application of Mg-HAP/BMP-2 matrixes in bone regeneration implants/scaffolds.

Molecular-level insight of hindered phenol AO-70/nitrile-butadiene rubber damping composites through a combination of a molecular dynamics simulation and experimental method

The damping properties of AO-70/NBR composites get a noteworthy increase with the introduction of AO-70—max tan δincreased by 66.9%.

Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies

The binding mode and binding free energy of the Saprolegnia monoica chitin synthase MIT domain with the POPA membrane have been studied by molecular simulation methods.

Functionalization of a Collagen-Hydroxyapatite Scaffold with Osteostatin to Facilitate Enhanced Bone Regeneration

Defects within bones caused by trauma and other pathological complications may often require the use of a range of therapeutics to facilitate tissue regeneration. A number of approaches have been widely utilized for the delivery of such therapeutics via physical encapsulation or chemical immobilization suggesting significant promise in the healing of bone defects. The study focuses on the chemical immobilization of osteostatin, a pentapeptide of the parathyroid hormone (PTHrP107-111), within a collagen-hydroxyapatite scaffold. The chemical attachment method via crosslinking supports as little as 4% release of the peptide from the scaffolds after 21 d whereas non-crosslinking leads to 100% of the peptide being released by as early as 4 d. In vitro characterization demonstrates that this cross-linking method of immobilization supports a pro-osteogenic effect on osteoblasts. Most importantly, when implanted in a critical-sized calvarial defect within a rat, these scaffolds promote significantly greater new bone volume and area compared to nonfunctionalized scaffolds (**p < 0.01) and an empty defect control (***p < 0.001). Collectively, this study suggests that such an approach of chemical immobilization offers greater spatiotemporal control over growth factors and can significantly modulate tissue regeneration. Such a system may be adopted for a range of different proteins and thus offers the potential for the treatment of various complex pathologies that require localized mediation of drug delivery.

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.

Effect of the Materials Properties of Hydroxyapatite Nanoparticles on Fibronectin Deposition and Conformation

Hydroxyapatite (HAP, Ca₁₀(PO₄)₆(OH)₂) nanoparticles with controlled materials properties have been synthesized through a two-step hydrothermal aging method to investigate fibronectin (Fn) adsorption. Two distinct populations of HAP nanoparticles have been generated: HAP1 particles had smaller size, plate-like shape, lower crystallinity, and more negative ζ potential than HAP2 particles. We then developed two-dimensional platforms containing HAP and Fn and analyzed both the amount and the conformation of Fn via Förster resonance energy transfer (FRET) at various HAP concentrations. Our FRET analysis reveals that larger amounts of more compact Fn molecules were adsorbed onto HAP1 than onto HAP2 particles. Additionally, our data show that the amount of compact Fn adsorbed increased with increasing HAP concentration due to the formation of nanoparticle agglomerates. We propose that both the surface chemistry of single nanoparticles and the size and morphology of HAP agglomerates play significant roles in the interaction of Fn with HAP. Collectively, our findings suggest that the HAP-induced conformational changes of Fn, a critical mechanotransducer protein involved in the communication of cells with their environment, will ultimately affect downstream cellular behaviors. These results have important implications for our understanding of organic-inorganic interactions in physiological and pathological biomineralization processes such as HAP-related inflammation.

Needle-Free Dermal Delivery of a Diphtheria Toxin CRM197 Mutant on Potassium-Doped Hydroxyapatite Microparticles

Injections with a hypodermic needle and syringe (HNS) are the current standard of care globally, but the use of needles is not without limitation. While a plethora of needle-free injection devices exist, vaccine reformulation is costly and presents a barrier to their widespread clinical application. To provide a simple, needle-free, and broad-spectrum protein antigen delivery platform, we developed novel potassium-doped hydroxyapatite (K-Hap) microparticles with improved protein loading capabilities that can provide sustained local antigen presentation and release. K-Hap showed increased protein adsorption over regular hydroxyapatite (P < 0.001), good structural retention of the model antigen (CRM197) with 1% decrease in α-helix content and no change in β-sheet content upon adsorption, and sustained release in vitro. Needle-free intradermal powder inoculation with K-Hap-CRM197 induced significantly higher IgG1 geometric mean titers (GMTs) than IgG2a GMTs in a BALB/c mouse model (P < 0.001) and induced IgG titer levels that were not different from the current clinical standard (P > 0.05), namely, alum-adsorbed CRM197 by intramuscular (i.m.) delivery. The presented results suggest that K-Hap microparticles may be used as a novel needle-free delivery vehicle for some protein antigens.

Investigation of alanine mutations affecting insulin-like growth factor (IGF) I binding to IGF binding proteins

Binding properties of wild type (WT) and six single amino acid substituted variants (E3A, E9A, D12A, D20A, F23A, and E58A) of insulin-like growth factor I (IGF-I) were analyzed with respect to their binding details to IGF binding proteins (IGFBPs) by molecular dynamics (MD) simulations. The binding sites and binding interactions on IGF-I and IGFBPs are screened and compared with the static X-ray structure. Electrostatic interaction is the primary driving force of the interaction between IGF-I and IGFBPs. Mutation may cause the rearrangement of binding sites, however, the unfolding of protein induced by mutation is not obvious in this work. We also provide the detailed picture of binding factors. And the results show that, whether the unfolding of helix occurs or not, the Ala mutation will change the molecular atmosphere of the binding interface by the rearrangement of conformation, and further affects the binding residues and binding interactions.

Surface energetics of the hydroxyapatite nanocrystal-water interface: a molecular dynamics study

Face-specific interfacial energies and structures of water at ionic crystal surfaces play a dominant role in a wide range of biological, environmental, technological, and industrial processes. Nanosized, plate-shaped crystals of calcium phosphate (CaP) with nonideal stoichiometry of hydroxyapatite (HAP, ideal stoichiometry Ca10(PO4)6(OH)2) comprise the inorganic component of bone and dentin. The crystal shape and size contribute significantly to these tissues' biomechanical properties. Plate-shaped HAP can be grown in the presence of biomolecules, whereas inorganically grown HAP crystals have a needlelike shape. Crystal morphology reflects the relative surface areas of the faces and, for an ideal inorganically grown crystal, should be governed by the surface energies of the faces with water. Interfacial energies and dynamics also affect biomolecule adsorption. Obtaining face-specific surface energies remains experimentally challenging because of the difficulty in growing large HAP single crystals. Here we employed molecular dynamics (MD) simulations to determine nanocrystalline HAP-water interfacial energies. The (100) face was found to be the most favorable energetically, and (110) and (004) were less hydrophilic. The trend in increasing interfacial energy was accompanied by a decrease in the average coordination number of water oxygen to surface calcium ions. The atomic-level geometry of the faces influenced interfacial energy by limiting lateral diffusion of water and by interrupting the hydrogen bond network. Such unfavorable interactions were limited on (100) compared to the other faces. These results provide a thermodynamic basis for the empirically observed trends in relative surface areas of HAP faces. The penetration of charged biomolecules through the interfacial water to form direct interactions with HAP faces, thus potentially influencing morphology, can also be rationalized.

Synthesis of carboxylic block copolymers via reversible addition fragmentation transfer polymerization for tooth erosion prevention

Dental professionals are seeing a growing population of patients with visible signs of dental erosion. The approach currently being used to address the problem typically leverages the enamel protection benefits of fluoride. In this report, an alternative new block copolymer with a hydrophilic polyacrylic acid (PAA) block and a hydrophobic poly(methyl methacrylate) (PMMA) block was developed to similarly reduce the mineral loss from enamel under acidic conditions. This series of PMMA-b-PAA block copolymers was synthesized by reversible addition fragmentation transfer (RAFT) polymerization. Their structures were characterized by gel permeation chromatography (GPC) and (1)H nuclear magnetic resonance (NMR) spectra. The molar fractions of acrylic acid (AA) in the final block copolymer were finely controlled from 0.25 to 0.94, and the molecular weight (Mn) of PMMA-b-PAA was controlled from 10 kDa to 90 kDa. The binding capability of the block copolymer with hydroxyapatite (HAP) was investigated by ultraviolet-visible spectroscopy (UV-Vis) and Fourier transform infrared (FTIR) spectroscopy. FTIR spectra confirmed that the PMMA-b-PAA block copolymer could bind to HAP via bridging bidentate bonds. Both UV-Vis and FTIR spectra additionally indicated that a high polymer concentration and low solution pH favored the polymer binding to HAP. The erosion-preventing efficacy of the PMMA-b-PAA block copolymer in inhibiting HAP mineral loss was quantitatively evaluated by atomic absorption spectroscopy (AAS). Based on the results, polymer treatment reduced the amount of calcium released by 27% to 30% in comparison with the unprotected samples. Scanning electron microscope (SEM) observations indicated that PMMA-b-PAA polymer treatment protected enamel from acid erosion. This new amphiphilic block copolymer has significant potential to be integrated into dentifrices or mouthrinses as an alternative non-fluoride ingredient to reduce tooth erosion.

Bioinspired amphiphilic phosphate block copolymers as non-fluoride materials to prevent dental erosion

Inspired by the fact that certain natural proteins, e.g. casein phosphopeptide or amelogenin, are able to prevent tooth erosion (mineral loss) and to enhance tooth remineralization, a synthetic amphiphilic diblock copolymer, containing a hydrophilic methacryloyloxyethyl phosphate block (MOEP) and a hydrophobic methyl methacrylate block (MMA), was designed as a novel non-fluoride agent to prevent tooth erosion under acidic conditions. The structure of the polymer, synthesized by reversible addition-fragment transfer (RAFT) polymerization, was confirmed by gel permeation chromatography (GPC), Fourier transform infrared spectroscopy (FTIR), and nuclear magnetic resonance spectroscopy (NMR). While the hydrophilic PMOEP block within the amphiphilic block copolymer strongly binds to the enamel surface, the PMMA block forms a hydrophobic shell to prevent acid attack on tooth enamel, thus preventing/reducing acid erosion. The polymer treatment not only effectively decreased the mineral loss of hydroxyapatite (HAP) by 36-46% compared to the untreated control, but also protected the surface morphology of the enamel specimen following exposure to acid. Additionally, experimental results confirmed that low pH values and high polymer concentrations facilitate polymer binding. Thus, the preliminary data suggests that this new amphiphilic diblock copolymer has the potential to be used as a non-fluoride ingredient for mouth-rinse or toothpaste to prevent/reduce tooth erosion.

Molecular dynamics study on the interaction between doxorubicin and hydrophobically modified chitosan oligosaccharide

Both π–π interactions and hydrophobic interactions were found to be essential for the loading of doxorubicin on hydrophobically modified chitosan oligosaccharides.