Does adsorption at hydroxyapatite surfaces induce peptide folding? Insights from large-scale B3LYP calculations

Aspartic Acid Binding on Hydroxyapatite Nanoparticles with Varying Morphologies Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulation

Hydroxyapatite (HAP) exhibits a highly oriented hierarchical structure in biological hard tissues. The formation and selective crystalline orientation of HAP is a process that involves functional biomineralization proteins abundant in acidic residues. To obtain insights into the process of HAP mineralization and acidic residue binding, synthesized HAP with specific lattice planes including (001), (100), and (011) are structurally characterized following the adsorption of aspartic acid (Asp). The adsorption affinity of Asp on HAP surfaces is evaluated quantitatively and demonstrates a high dependency on the HAP morphological form. Among the synthesized HAP nanoparticles (NPs), Asp exhibits the strongest adsorption affinity to short HAP nanorods, which are composed of (100) and (011) lattice planes, followed by nanosheets with a preferential expression of the (001) facet, to which Asp displays a similar but slightly lower binding affinity. HAP nanowires, with the (100) lattice plane preferentially developed, show significantly lower affinity to Asp and evidence of multilayer adsorption compared to the previous two types of HAP NPs. A combination of solid-state NMR (SSNMR) techniques including 13C and 15N CP-MAS, relaxation measurements and 13C-31P Rotational Echo DOuble Resonance (REDOR) is utilized to characterize the molecular structure and dynamics of Asp-HAP bionano interfaces with 13C- and 15N-enriched Asp. REDOR is used to determine 13C-31P internuclear distances, providing insight into the Asp binding geometry where stronger 13C-31P dipolar couplings correlate with binding affinity determined from Langmuir isotherms. The carboxyl sites are identified as the primary binding groups, facilitated by their interaction with surface calcium sites. The Asp chelation conformations revealed by SSNMR are further refined with molecular dynamics (MD) simulation where specific models strongly agree between the SSNMR and MD models for the various surfaces.

On the stability of peptide secondary structures on the TiO2 (101) anatase surface: a computational insight

The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and β-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO₂ (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO₂ surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO₂ (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO₂ surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO₂ surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

Defect Induced Charge Redistribution and Enhanced Adsorption of Lysozyme on Hydroxyapatite for Efficient Antibacterial Activity

Defects in hydroxyapatite (HA) have attracted increasing research interest due to their significant functions to increase the bioactivity and antibacterial ability of hard-tissue implants. However, little is known about the natural property and functional mechanism of the defects in HA. Herein, we reported on the defect property concerned with the coordination state and charge distribution in Al doped HA, as well as the consequent interface and protein capture ability for improved antibacterial activity. Systemic investigations suggested that Al replacing Ca in HA induced coordination defect with decreased coordination number and bond distance, caused charge transfer and redistribution of surrounding O atom and resulted in an increase in negative charge of coordinated O atoms. These O atoms coordinated with Al further served as docking sites for lysozyme molecules via electrostatic and H-bonding interaction. The capacity of lysozyme adsorption for Al-HA increased approximately 10-fold more than that of HA, which significantly increased the antibacterial activity through lysozyme-catalyzed splitting of cell wall of bacteria. Moreover, in vitro studies indicated that Al-HA materials showed good cytocompatibility. These findings not only provided new insights into the important effect of defects on the performances of HA biomaterials by modulation of the coordination state, charge distribution, and chemical activity, but also proposed a promising method for efficient antibacterial activity of HA biomaterials.

Environment-controlled water adsorption at hydroxyapatite/collagen interfaces

Water contributes to the structure of bone by coupling hydroxyapatite to collagen over the hierarchical levels of tissue organization. Bone water exists in two states, bound or mobile, each accomplishing different roles. Although many experimental studies show that the amount of bound water correlates with bone strength, a molecular understanding of the interactions between hydroxyapatite, collagen and water is missing. In this work, we unveil the water adsorption properties of bone tissues at the nanoscale using advanced density functional theory methods. We demonstrate that environmental factors such as collagen conformation or degree of confinement, rather than the surface itself, dictate the adsorption mode, strength and density of water on hydroxyapatite. While the results derived in this paper come from a simplified model of bone tissues, they are consistent with experimental observations and constitute a reasonable starting point for more realistic models of bone tissues. For example, we show that environmental changes expected in aging bone lead to reduced water adsorption capabilities, which is consistent with weaker bones at the macroscale. Our findings provide a new interpretation of molecular interactions in bone tissues with the potential to impact bone repair strategies.

Hydroxylapatite and Related Minerals in Bone and Dental Tissues: Structural, Spectroscopic and Mechanical Properties from a Computational Perspective

Hard tissues (e.g., bone, enamel, dentin) in vertebrates perform various and different functions, from sustaining the body to haematopoiesis. Such complex and hierarchal tissue is actually a material composite whose static and dynamic properties are controlled by the subtle physical and chemical interplay between its components, collagen (main organic part) and hydroxylapatite-like mineral. The knowledge needed to fully understand the properties of bony and dental tissues and to develop specific applicative biomaterials (e.g., fillers, prosthetics, scaffolds, implants, etc.) resides mostly at the atomic scale. Among the different methods to obtains such detailed information, atomistic computer simulations (in silico) have proven to be both corroborative and predictive tools in this subject. The authors have intensively worked on quantum mechanical simulations of bioapatite and the present work reports a detailed review addressed to the crystal-chemical, physical, spectroscopic, mechanical, and surface properties of the mineral phase of bone and dental tissues. The reviewed studies were conducted at different length and time scales, trying to understand the features of hydroxylapatite and biological apatite models alone and/or in interaction with simplified collagen-like models. The reported review shows the capability of the computational approach in dealing with complex biological physicochemical systems, providing accurate results that increase the overall knowledge of hard tissue science.

Synthesis of monodisperse rod-shaped silica particles through biotemplating of surface-functionalized bacteria

Mesoporous silica particles of controlled size and shape are potentially beneficial for many applications, but their usage may be limited by the complex procedure of fabrication. Biotemplating provides a facile approach to synthesize materials with desired shapes. Herein, a bioinspired design principle is adopted through displaying silaffin-derived 5R5 proteins on the surface of Escherichia coli by genetic manipulations. The genetically modified Escherichia coli provides a three-dimensional template to regulate the synthesis of rod-shaped silica. The silicification is initiated on the cell surface under the functionality of 5R5 proteins and subsequentially the inner space is gradually filled. Density functional theory simulation reveals the interfacial interactions between silica precursors and R5 peptides at the atomic scale. There is a large conformation change of this protein during biosilicification. Electrostatic interactions contribute to the high affinity between positively charged residues (Lys4, Arg16, Arg17) and negatively charged tetraethyl orthosilicate. Hydrogen bonds develop between Arg16 (OH), Arg17 (OH and NH), Leu19 (OH) residues and the forming silica agglomerates. In addition, the resulting rod-shaped silica copy of the bacteria can transform into mesoporous SiOx nanorods composed of carbon-coated nanoparticles after carbonization, which is shown to allow superior lithium storage performance.

Towards the control of the biological identity of nanobiomaterials: Impact of the structure of 011¯0 surface terminations of nanohydroxyapatite on the conformation of adsorbed proteins

High-resolution transmission electron microscopy, ζ-potential and in-situ IR spectroscopy of adsorbed CO were combined for elucidating the ratio between {011¯0}_ Ca-rich: {011¯0}_ P-rich terminations of {011¯0} facets, i.e. the surfaces with the highest morphological importance, in two nanohydroxyapatite samples. Bovine serum albumin was found to form at least a monolayer on the surface left accessible to protein molecules by the agglomeration of nanoparticles when suspended in the buffered incubation medium. Noticeably, the conformation of adsorbed proteins appeared sensitive to the ratio between the two types of {011¯0} terminations, also resulting in a difference in the surface exposed toward the exterior by the adsorbed protein layer(s).

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.

Rational Design of Iron Oxide Binding Peptide Tags

Owing to their extraordinary magnetic properties and low-cost production, iron oxide nanoparticles (IONs) are in the focus of research. In order to better understand interactions of IONs with biomolecules, a tool for the prediction of the propensity of different peptides to interact with IONs is of great value. We present an effective implicit surface model (EISM), which includes several interaction models. Electrostatic interactions, van der Waals interactions, and entropic effects are considered for the theoretical calculations. However, the most important parameter, a surface accessible area force field contribution term, derives directly from experimental results on the interactions of IONs and peptides. Data from binding experiments of ION agglomerates to different peptides immobilized on cellulose membranes have been used to parameterize the model. The work was carried out under defined environmental conditions; hence, effects because of changes, for example structure or solubility by changing the surroundings, are not included. EISM enables researchers to predict the binding of peptides to IONs, which we then verify with further peptide array experiments in an iterative optimization process also presented here. Negatively charged peptides were identified as best binders for IONs in Tris buffer. Furthermore, we investigated the constitution of peptides and how the amount and position of several amino acid side chains affect peptide-binding. The incorporation of glycine leads to higher binding scores compared to the incorporation of cysteine in negatively charged peptides.

The synthesis of super-small nano hydroxyapatite and its high adsorptions to mixed heavy metallic ions

A "molecular cage" was possibly built in glucose alkaline solution to limit the chemical reaction in a tiny space to control the size and morphology of HA nanoparticles. A possible reaction mechanism of HA nanoparticles confined space synthesis was proposed in this work. The super-small HA nanoparticles were successfully obtained in the first time in mild and green condition which had a 7 nm diameter. The adsorptions to Pb²⁺, Zn²⁺, Ni²⁺, Cd²⁺ ions in their mixture solution by the synthesized HA nanoparticles were studied. The adsorbent showed huge adsorption capacities for the targets (Pb²⁺ = 3289 mg/g, Zn²⁺ = 3150 mg/g, Ni²⁺ = 3061 mg/g and Cd²⁺ = 2784 mg/g), which indicated an excellent performance of the synthesized nano material in water treatment. Freundlich equation analysis and SEM images of the adsorption products suggested multilayer adsorptions to the targets, and a new recrystalline type adsorption on the surface of the host was found. Some Ca atoms in HA nanoparticles were also found to be substituted by the heavy metallic elements in the initial stage of the adsorptions. The synthesized nano material exhibits better application prospect in wastewater treatment field for its easy synthesis, low-cost and environmental friendly properties.

Binding patterns of homo-peptides on bare magnetic nanoparticles: insights into environmental dependence

Magnetic nanoparticles (MNP) are intensively investigated for applications in nanomedicine, catalysis and biotechnology, where their interaction with peptides and proteins plays an important role. However, the characterisation of the interaction of individual amino acids with MNP remains challenging. Here, we classify the affinity of 20 amino acid homo-hexamers to unmodified iron oxide nanoparticles using peptide arrays in a variety of conditions as a basis to identify and rationally design selectively binding peptides. The choice of buffer system is shown to strongly influence the availability of peptide binding sites on the MNP surface. We find that under certain buffer conditions peptides of different charges can bind the MNP and that the relative strength of the interactions can be modulated by changing the buffer. We further present a model for the competition between the buffer and the MNP's electrostatically binding to the adsorption sites. Thereby, we demonstrate that the charge distribution on the surface can be used to correlate the binding of positively and negatively charged peptides to the MNP. This analysis enables us to engineer the binding of MNP on peptides and contribute to better understand the bio-nano interactions, a step towards the design of affinity tags for advanced biomaterials.

How High Concentrations of Proteins Stabilize the Amorphous State of Calcium Orthophosphate: A Solid-State Nuclear Magnetic Resonance (NMR) Study of the Casein Case

Understanding how proteins stabilize amorphous calcium ortho-phosphate (ACP) phases is of great importance in biology and for pharmaceutical or food applications. Until now, most of the former investigations about ACP-protein stability and equilibrium were performed under conditions where ACP colloidal nanoclusters are surrounded by low to moderate concentrations of peptides or proteins (15-30 g L^-1). As a result, the question of ACP-protein interactions in highly concentrated protein systems has clearly been overlooked, whereas it corresponds to actual industrial conditions such as drying or membrane filtration in the dairy industry for instance. In this study, the structure of an ACP phase is monitored in association with one model phosphorylated protein (casein) using solid-state nuclear magnetic resonance (ssNMR) under two conditions of high protein concentration (300 and 400 g L^-1). At both concentrations and at 25 °C, it is found that the caseins maintain the mineral phase in an amorphous form with no detectable influence on its structure or size. Interestingly, and in both cases, a significant amount of the nonphosphorylated side chains interacts with ACP through hydrogen bonds. The number of these interacting side chains is found to be higher at the highest casein concentration. At 45 °C, which is a destabilizing temperature of ACP under protein-free conditions, the amorphous structure of the mineral phase is partially transformed at a casein concentration of 300 g L^-1, while it remains almost intact at a casein concentration of 400 g L^-1. Therefore, these results clearly indicate that increasing the concentration of proteins favors ACP-protein interactions and stabilizes the ACP clusters more efficiently.

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.

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.

Facet selectivity in gold binding peptides: exploiting interfacial water structure

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.

Affinity of the interface between hydroxyapatite (0001) and titanium (0001) surfaces: a first-principles investigation

A basic understanding of the affinity between the hydroxyapatite (HA) and α-Ti surfaces is obtained through electronic structure calculations by first-principles method. The surface energies of HA(0001), HA (011̅0), HA (101̅1), and Ti(0001) surfaces have been calculated. The HA(0001) presents the most thermodynamically stable of HA. The HA/Ti interfaces were constructed by two kinds of interface models, the single interface (denoted as SI) and the double-interface (denoted as DI). Two methods, the full relaxation and the UBER, were applied to determine the interfacial separation and the atomic arrangement in the interfacial zone. The works of adhesion of interfaces with various stoichiometric HA surfaces were evaluated. For the HA(0001)/Ti(0001) interfaces, the work of adhesion is strongly dependent on the chemical environment of the HA surface. The values are -2.33, -1.52, and -0.80 J/m(2) for the none-, single-, and double-Ca terminated HA/Ti interfaces, respectively. The influence of atomic relaxation on the work of adhesion and interface separation is discussed. Full relaxation results include -1.99 J/m(2) work of adhesion and 0.220 nm separation between HA and Ti for the DI of 1-Ca-HA/Ti interface, while they are -1.14 J/m(2) and 0.235 nm by partial relaxation. Analysis of electronic structure reveals that charge transfer between HA and Ti slabs occurs during the formation of the HA/Ti interface. The transfer generates the Ti-O or Ti-Ca bonds across the interface and drives the HA/Ti interface system to metallic characteristic. The energetically favorable interfaces are formed when the outmost layer of HA comprises more O atoms at the interface.

Binding is responsible for exceptional hardness in polyethylene/silicalite nanocomposite materials

Mechanical properties of PESIL – a novel polyethylene/silicalite nanocomposite material – were studied in detail through ab initio calculations.

New developments in polymer-controlled, bioinspired calcium phosphate mineralization from aqueous solution

The polymer-controlled and bioinspired precipitation of inorganic minerals from aqueous solution at near-ambient or physiological conditions avoiding high temperatures or organic solvents is a key research area in materials science. Polymer-controlled mineralization has been studied as a model for biomineralization and for the synthesis of (bioinspired and biocompatible) hybrid materials for a virtually unlimited number of applications. Calcium phosphate mineralization is of particular interest for bone and dental repair. Numerous studies have therefore addressed the mineralization of calcium phosphate using a wide variety of low- and high-molecular-weight additives. In spite of the growing interest and increasing number of experimental and theoretical data, the mechanisms of polymer-controlled calcium phosphate mineralization are not entirely clear to date, although the field has made significant progress in the last years. A set of elegant experiments and calculations has shed light on some details of mineral formation, but it is currently not possible to preprogram a mineralization reaction to yield a desired product for a specific application. The current article therefore summarizes and discusses the influence of (macro)molecular entities such as polymers, peptides, proteins and gels on biomimetic calcium phosphate mineralization from aqueous solution. It focuses on strategies to tune the kinetics, morphologies, final dimensions and crystal phases of calcium phosphate, as well as on mechanistic considerations.

Using the RosettaSurface algorithm to predict protein structure at mineral surfaces

Determination of protein structure on mineral surfaces is necessary to understand biomineralization processes toward better treatment of biomineralization diseases and design of novel protein-synthesized materials. To date, limited atomic-resolution data have hindered experimental structure determination for proteins on mineral surfaces. Molecular simulation represents a complementary approach. In this chapter, we review RosettaSurface, a computational structure prediction-based algorithm designed to broadly sample conformational space to identify low-energy structures. We summarize the computational approaches, the published applications, and the new releases of the code in the Rosetta 3 framework. In addition, we provide a protocol capture to demonstrate the practical steps to employ RosettaSurface. As an example, we provide input files and output data analysis for a previously unstudied mineralization protein, osteocalcin. Finally, we summarize ongoing challenges in energy function optimization and conformational searching and suggest that the fusion between experiment and calculation is the best route forward.

Hydroxylapatite nanoparticles: fabrication methods and medical applications

Hydroxylapatite (or hydroxyapatite, HAp) exhibits excellent biocompatibility with various kinds of cells and tissues, making it an ideal candidate for tissue engineering, orthopedic and dental applications. Nanosized materials offer improved performances compared with conventional materials due to their large surface-to-volume ratios. This review summarizes existing knowledge and recent progress in fabrication methods of nanosized (or nanostructured) HAp particles, as well as their recent applications in medical and dental fields. In section 1, we provide a brief overview of HAp and nanoparticles. In section 2, fabrication methods of HAp nanoparticles are described based on the particle formation mechanisms. Recent applications of HAp nanoparticles are summarized in section 3. The future perspectives in this active research area are given in section 4.