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

Integrating biophysical modeling, quantum computing, and AI to discover plastic-binding peptides that combat microplastic pollution

Methods are needed to mitigate microplastic (MP) pollution to minimize their harm to the environment and human health. Given the ability of polypeptides to adsorb strongly to materials of micro- or nanometer size, plastic-binding peptides (PBPs) could help create bio-based tools for detecting, filtering, or degrading MNP pollution. However, the development of such tools is prevented by the lack of PBPs. In this work, we discover and evaluate PBPs for several common plastics by combining biophysical modeling, molecular dynamics (MD), quantum computing, and reinforcement learning. We frame peptide affinity for a given plastic through a Potts model that is a function of the amino acid sequence and then search for the amino acid sequences with the greatest predicted affinity using quantum annealing. We also use proximal policy optimization to find PBPs with a broader range of physicochemical properties, such as isoelectric point or solubility. Evaluation of the discovered PBPs in MD simulations demonstrates that the peptides have high affinity for two of the plastics: polyethylene and polypropylene. We conclude by describing how our computational approach could be paired with experimental approaches to create a nexus for designing and optimizing peptide-based tools that aid the detection, capture, or biodegradation of MPs. We thus hope that this study will aid in the fight against MP pollution.

Hybrid Hydroxyapatite-Metal Complex Materials Derived from Amino Acids and Nucleobases

Calcium phosphates (CaPs) and their substituted derivatives encompass a large number of compounds with a vast presence in nature that have aroused a great interest for decades. In particular, hydroxyapatite (HAp, Ca10(OH)2(PO4)6) is the most abundant CaP mineral and is significant in the biological world, at least in part due to being a major compound in bones and teeth. HAp exhibits excellent properties, such as safety, stability, hardness, biocompatibility, and osteoconductivity, among others. Even some of its drawbacks, such as its fragility, can be redirected thanks to another essential feature: its great versatility. This is based on the compound's tendency to undergo substitutions of its constituent ions and to incorporate or anchor new molecules on its surface and pores. Thus, its affinity for biomolecules makes it an optimal compound for multiple applications, mainly, but not only, in biological and biomedical fields. The present review provides a chemical and structural context to explain the affinity of HAp for biomolecules such as proteins and nucleic acids to generate hybrid materials. A size-dependent criterium of increasing complexity is applied, ranging from amino acids/nucleobases to the corresponding macromolecules. The incorporation of metal ions or metal complexes into these functionalized compounds is also discussed.

Graphitic nanoflakes modulate the structure and binding of human amylin

Human amylin is an inherently disordered protein whose ability to form amyloid fibrils is linked to the onset of type II diabetes. Graphitic nanomaterials have potential in managing amyloid diseases as they can disrupt protein aggregation processes in biological settings, but optimising these materials to prevent fibrillation is challenging. Here, we employ bias-exchange molecular dynamics simulations to systematically study the structure and adsorption preferences of amylin on graphitic nanoflakes that vary in their physical dimensions and surface functionalisation. Our findings reveal that nanoflake size and surface oxidation both influence the structure and adsorption preferences of amylin. The purely hydrophobic substrate of pristine graphene (PG) nanoflakes encourages non-specific protein adsorption, leading to unrestricted lateral mobility once amylin adheres to the surface. Particularly on larger PG nanoflakes, this induces structural changes in amylin that may promote fibril formation, such as the loss of native helical content and an increase in β-sheet character. In contrast, oxidised graphene nanoflakes form hydrogen bonds between surface oxygen sites and amylin, and as such restricting protein mobility. Reduced graphene oxide (rGO) flakes, featuring lower amounts of surface oxidation, are amphiphilic and exhibit substantial regions of bare carbon which promote protein binding and reduced conformational flexibility, leading to conservation of the native structure of amylin. In comparison, graphene oxide (GO) nanoflakes, which are predominantly hydrophilic and have a high degree of surface oxidation, facilitate considerable protein structural variability, resulting in substantial contact area between the protein and GO, and subsequent protein unfolding. Our results indicate that tailoring the size, oxygen concentration and surface patterning of graphitic nanoflakes can lead to specific and robust protein binding, ultimately influencing the likelihood of fibril formation. These atomistic insights provide key design considerations for the development of graphitic nanoflakes that can modulate protein aggregation by sequestering protein monomers in the biological environment and inhibit conformational changes linked to amyloid fibril formation.

In silico discovery of potential PPI inhibitors for anti-lung cancer activity by targeting the CCND1-CDK4 complex via the P21 inhibition mechanism

Non-Small Cell Lung Cancer (NSCLC) is a prevalent and deadly form of lung cancer worldwide with a low 5-year survival rate. Current treatments have limitations, particularly for advanced-stage patients. P21, a protein that inhibits the CCND1-CDK4 complex, plays a crucial role in cell proliferation. Computer-Aided Drug Design (CADD) based on pharmacophores can screen and design PPI inhibitors targeting the CCND1-CDK4 complex. By analyzing known inhibitors, key pharmacophores are identified, and computational methods are used to screen potential PPI inhibitors. Molecular docking, pharmacophore matching, and structure-activity relationship studies optimize the inhibitors. This approach accelerates the discovery of CCND1-CDK4 PPI inhibitors for NSCLC treatment. Molecular dynamics simulations of CCND1-CDK4-P21 and CCND1-CDK4 complexes showed stable behavior, comprehensive sampling, and P21's impact on complex stability and hydrogen bond formation. A pharmacophore model facilitated virtual screening, identifying compounds with favorable binding affinities. Further simulations confirmed the stability and interactions of selected compounds, including 513457. This study demonstrates the potential of CADD in optimizing PPI inhibitors targeting the CCND1-CDK4 complex for NSCLC treatment. Extended simulations and experimental validations are necessary to assess their efficacy and safety.

Interaction of Statherin-Derived Peptide with the Surface of Hydroxyapatite: Perspectives Based on Molecular Dynamics Simulations

INTRODUCTION

Statherin-derived peptide (StatpSpS) has shown promise against erosive tooth wear. To elucidate its interaction with the hydroxyapatite (HAP) surface, the mechanism related to adsorption of this peptide with HAP was investigated through nanosecond-long all-atom molecular dynamics simulations.

METHODS

StatpSpS was positioned parallel to the HAP surface in 2 orientations: 1 - neutral and negative residues facing the surface and 2 - positive residues facing the surface. A system containing StatpSpS without HAP was also simulated as control. In the case of systems with HAP, both partially restrained surface and unrestrained surface were constructed. Structural analysis, interaction pattern, and binding-free energy were calculated.

RESULTS

In the peptide system without the HAP, there were some conformational changes during the simulation. In the presence of the surface, only moderate changes were observed. Many residues exhibited short and stable distances to the surface, indicating strong interaction. Specially, the residues ASP1 and SER2 have an important role to anchor the peptide to the surface, with positively charged residues, mainly arginine, playing a major role in the further stabilization of the peptide in an extended conformation, with close contacts to the HAP surface.

CONCLUSION

The interaction between StatpSpS and HAP is strong, and the negative charged residues are important to the anchoring of the peptide in the surface, but after the initial placement the peptide rearranges itself to maximize the interactions between positive charged residues.

A novel amelogenesis-inspired hydrogel composite for the remineralization of enamel non-cavitated lesions

Enamel non-cavitated lesions (NCLs) are subsurface enamel porosity from carious demineralization. The developed enamel cannot repair itself once NCLs occurs. The regeneration of mineral crystals in a biomimetic environment is an effective way to repair enamel subsurface defects. Previously, an amelogenin-derived peptide named QP5 was proven to repair demineralized enamel. In this work, inspired by amelogenesis, a novel biomimetic hydrogel composite containing the QP5 peptide and bioactive glass (BG) was designed, in which QP5 could promote enamel remineralization by guiding the calcium and phosphorus ions provided by BG. Also, BG could adjust the mineralization micro-environment to alkalinity, simulating the pH regulation of ameloblasts during enamel maturity. The BQ hydrogel composite showed biosafety and possessed capacity for enamel binding, ion release and pH buffering. Enamel NCLs treated with the BQ hydrogel composite showed a higher reduction in lesion depth and mineral loss both in vitro and in vivo. Moreover, compared to the hydrogels containing only BG or QP5, groups treated with the BQ hydrogel composite attained more surface microhardness recovery and color recovery, exhibiting resistance to erosion and abrasion of the remineralization layer. We envision that the BQ hydrogel composite can provide a biomimetic micro-environment to favor enamel remineralization, thus reducing the lesion depth and increasing the mineral content as a promising biomimetic material for enamel NCLs.

Hierarchical Structure and Properties of the Bone at Nano Level

Bone is a highly hierarchical complex structure that consists of organic and mineral components represented by collagen molecules (CM) and hydroxyapatite crystals (HAC), respectively. The nanostructure of bone can significantly affect its mechanical properties. There is a lack of understanding how collagen fibrils (CF) in different orientations may affect the mechanical properties of the bone. The objective of this study is to investigate the effect of interaction, orientation, and hydration on atomic models of the bone composed of collagen helix (CH) and HAC, using molecular dynamics simulations and therefrom bone-related disease origins. The results demonstrate that the mechanical properties of the bone are affected significantly by the orientation of the CF attributed to contact areas at 0° and 90° models. The molecular dynamics simulation illustrated that there is significant difference (p < 0.005) in the ultimate tensile strength and toughness with respect to the orientation of the hydrated and un-hydrated CF. Additionally, the results indicated that having the force in a longitudinal direction (0°) provides more strength compared with the CF in the perpendicular direction (90°). Furthermore, the results show that substituting glycine (GLY) with any other amino acid affects the mechanical properties and strength of the CH, collagen−hydroxyapatite interface, and eventually affects the HAC. Generally, hydration dramatically influences bone tissue elastic properties, and any change in the orientation or any abnormality in the atomic structure of either the CM or the HAC would be the main reason of the fragility in the bone, affecting bone pathology.

Stable Binding Conformations of Polymaleic and Polyacrylic Acids at a Calcite Surface in the Presence of Countercations: A Metadynamics Study

Elucidating the stable binding conformations of additives at the surface of CaCO3 crystals is essential to biomineralization, scale inhibition, and materials technology. However, accomplishing this by experimental means is rather difficult. In this study, molecular dynamics simulations based on a metadynamics approach were conducted to elucidate the stable binding conformations of a deprotonated polymaleic acid (PMA) additive and two deprotonated poly(acrylic acid) (PAA) additives with different polymerization degrees in the presence of various countercations at a hydrated calcite (104) surface. The simulated free-energy surfaces suggested the existence of several slightly different stable binding conformations for each additive. The appearance of these distinct binding conformations is speculated to originate from different balances of interactions between the additive, the calcite surface, and the countercations. The binding conformations and binding stabilities at the calcite surface were affected by the countercations, with Ca2+ ions producing a more pronounced effect than Na+ ions. Furthermore, the simulation results suggested that the binding stability at the calcite surface was higher for the PMA additive than for the PAA additives, and the PAA additive with a polymerization degree of 10 displayed a binding stability that was similar to or lower than that of the PAA additive with a polymerization degree of 5. The present simulation method provides a new strategy for analyzing the binding conformations of complex additives at material surfaces, developing additives that stably bind to these surfaces, and designing additives to control crystal growth.

Understanding the Adhesion Mechanism of Hydroxyapatite-Binding Peptide

Understanding the interactions between the protein collagen and hydroxyapatite is of high importance for understanding biomineralization and bone formation. Here, we undertook a reductionist approach and studied the interactions between a short peptide and hydroxyapatite. The peptide was selected from a phage-display library for its high affinity to hydroxyapatite. To study its interactions with hydroxyapatite, we performed an alanine scan to determine the contribution of each residue. The interactions of the different peptide derivatives were studied using a quartz crystal microbalance with dissipation monitoring and with single-molecule force spectroscopy by atomic force microscopy. Our results suggest that the peptide binds via electrostatic interactions between cationic moieties of the peptide and the negatively charged groups on the crystal surface. Furthermore, our findings show that cationic residues have a crucial role in binding. Using molecular dynamics simulations, we show that the peptide structure is a contributing factor to the adhesion mechanism. These results suggest that even small conformational changes can have a significant effect on peptide adhesion. We suggest that a bent structure of the peptide allows it to strongly bind hydroxyapatite. The results presented in this study improve our understanding of peptide adhesion to hydroxyapatite. On top of physical interactions between the peptide and the surface, peptide structure contributes to adhesion. Unveiling these processes contributes to our understanding of more complex biological systems. Furthermore, it may help in the design of de novo peptides to be used as functional groups for modifying the surface of hydroxyapatite.

Hydroxyapatite-decorated Fmoc-hydrogel as a bone-mimicking substrate for osteoclast differentiation and culture

Hydrogels are water-swollen networks with great potential for tissue engineering applications. However, their use in bone regeneration is often hampered due to a lack of materials' mineralization and poor mechanical properties. Moreover, most studies are focused on osteoblasts (OBs) for bone formation, while osteoclasts (OCs), cells involved in bone resorption, are often overlooked. Yet, the role of OCs is pivotal for bone homeostasis and aberrant OC activity has been reported in several pathological diseases, such as osteoporosis and bone cancer. For these reasons, the aim of this work is to develop customised, reinforced hydrogels to be used as material platform to study cell function, cell-material interactions and ultimately to provide a substrate for OC differentiation and culture. Here, Fmoc-based RGD-functionalised peptide hydrogels have been modified with hydroxyapatite nanopowder (Hap) as nanofiller, to create nanocomposite hydrogels. Atomic force microscopy showed that Hap nanoparticles decorate the peptide nanofibres with a repeating pattern, resulting in stiffer hydrogels with improved mechanical properties compared to Hap- and RGD-free controls. Furthermore, these nanocomposites supported adhesion of Raw 264.7 macrophages and their differentiation in 2D to mature OCs, as defined by the adoption of a typical OC morphology (presence of an actin ring, multinucleation, and ruffled plasma membrane). Finally, after 7 days of culture OCs showed an increased expression of TRAP, a typical OC differentiation marker. Collectively, the results suggest that the Hap/Fmoc-RGD hydrogel has a potential for bone tissue engineering, as a 2D model to study impairment or upregulation of OC differentiation. STATEMENT OF SIGNIFICANCE: Altered osteoclasts (OC) function is one of the major cause of bone fracture in the most commonly skeletal disorders (e.g. osteoporosis). Peptide hydrogels can be used as a platform to mimic the bone microenvironment and provide a tool to assess OC differentiation and function. Moreover, hydrogels can incorporate different nanofillers to yield hybrid biomaterials with enhanced mechanical properties and improved cytocompatibility. Herein, Fmoc-based RGD-functionalised peptide hydrogels were decorated with hydroxyapatite (Hap) nanoparticles to generate a hydrogel with improved rheological properties. Furthermore, they are able to support osteoclastogenesis of Raw264.7 cells in vitro as confirmed by morphology changes and expression of OC-markers. Therefore, this Hap-decorated hydrogel can be used as a template to successfully differentiate OC and potentially study OC dysfunction.

Challenges and solutions in polymer drug delivery for bacterial biofilm treatment: A tissue-by-tissue account

To tackle the emerging antibiotic resistance crisis, novel antimicrobial approaches are urgently needed. Bacterial communities (biofilms) are a particular concern in this context. Biofilms are responsible for most human infections and are inherently less susceptible to antibiotic treatments. Biofilms have been linked with several challenging chronic diseases, including implant-associated osteomyelitis and chronic wounds. The specific local environments present in the infected tissues further contribute to the rise in antibiotic resistance by limiting the efficacy of systemic antibiotic therapies and reducing drug concentrations at the infection site, which can lead to reoccurring infections. To overcome the shortcomings of systemic drug delivery, encapsulation within polymeric carriers has been shown to enhance antimicrobial efficacy, permeation and retention at the infection site. In this Review, we present an overview of current strategies for antimicrobial encapsulation within polymeric carriers, comparing challenges and solutions on a tissue-by-tissue basis. We compare challenges and proposed drug delivery solutions from the perspective of the local environments for biofilms found in oral, wound, gastric, urinary tract, bone, pulmonary, vaginal, ocular and middle/inner ear tissues. We will also discuss future challenges and barriers to clinical translation for these therapeutics. The following Review demonstrates there is a significant imbalance between the research focus being placed on different tissue types, with some targets (oral and wound biofims) being extensively more studied than others (vaginal and otitis media biofilms and endocarditis). Furthermore, the importance of the local tissue environment when selecting target therapies is demonstrated, with some materials being optimal choices for certain sites of bacterial infection, while having limited applicability in others.

An enamel-inspired bioactive material with multiscale structure and antibacterial adhesion property

Conventional dental materials lack of the hierarchical architecture of enamel that exhibits excellent intrinsic-extrinsic mechanical properties. Moreover, restorative failures frequently occur due to physical and chemical mismatch between artificial materials and native dental hard tissue followed by recurrent caries which is caused by sugar-fermenting, acidogenic bacteria invasion of the defective cite. In order to resolve the limitations of the conventional dental materials, the aim of this study was to establish a non-cell-based biomimetic strategy to fabricate a novel bioactive material with enamel-like structure and antibacterial adhesion property. The evaporation-based, bottom-up and self-assembly method with layer-by-layer technique were used to form a large-area fluorapatite crystal layer containing antibacterial components. The multilayered structure was constructed by hydrothermal growth of the fluorapatite crystal layer and highly conformal adsorption to the crystal surface of a polyelectrolyte matrix film. Characterization and mechanical assessment demonstrated that the synthesized bioactive material resembled the native enamel in chemical components, mechanical properties and crystallographic structure. Antibacterial and cytocompatibility evaluation demonstrated that this material had the antibacterial adhesion property and biocompatibility. In combination with the molecular dynamics simulations to reveal the effects of variables on the crystallization mechanism, this study brings new prospects for the synthesis of enamel-inspired materials.

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A simple chemistry approach was offered to synthesize a enamel-like material without using cells or proteins.

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A macroscopic bioactive material resembled the native enamel with the antibacterial adhension propery was fabricated.

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Combining experiments and molecular dynamics simulations revealed effects of variables on the crystallization mechanism.

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ∼ 10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. The findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

A Novel Strategy for Caries Management: Constructing an Antibiofouling and Mineralizing Dual-Bioactive Tooth Surface

Existing single-functional agents against dental caries are inadequate in antibacterial performance or mineralization balance. This problem can be resolved through a novel strategy, namely, the construction of an antibiofouling and mineralizing dual-bioactive tooth surface by grafting a dentotropic moiety to an antimicrobial peptide. The constructed bioactive peptide can strongly adsorb onto the tooth surface and has beneficial functions in a myriad of ways. It inhibits cariogenic bacteria Streptococcus mutans adhesion, kills planktonic S. mutans, and destroys the S. mutans biofilm on the tooth surface. It also protects teeth from demineralization in acidic environments, and induces self-healing regeneration in the remineralization environment. Molecular dynamics simulations elucidate the main adsorption mechanism that the positively charged amino acid residues in the bioactive peptide bind to phosphate groups on the tooth surface, and the main mineralization mechanism that the negative charges on the outermost layer of the bioactive peptide repel acetic acid ions and attract calcium ions as nucleation sites for remineralization. This study suggests that this in-house synthesized dual-bioactive peptide is a promising functional agent to prevent dental caries, and is effective in inducing in situ self-healing remineralization for the treatment of decayed teeth.

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.

Unraveling the mechanism for an amelogenin-derived peptide regulated hydroxyapatite mineralization via specific functional domain identification

Amelogenin and its various derived peptides play important roles in promoting biomimetic mineralization of enamel. Previously, an amelogenin-derived peptide named QP5 was proved to be able to repair demineralized enamel. The objective here was to interpret the mechanism of QP5 by elucidating the specific function of each domain for further sequence and efficacy improvement. Peptide QP5 was separated into domains (QPX)5 and C-tail. (QPX)3 was also synthesized to investigate how QPX repeats affect the mineralization process. Circular dichroism spectroscopy showed that two (QPX) repeats adopted a β-sheet structure, while C-tail exhibited a disordered structure. (QPX)5 showed more absorption in confocal laser scanning microscopy observation and a higher K value in Langmuir adsorption isotherms compared to C-tail, while (QPX)3 with better hydropathy had greater adsorption capability than (QPX)5. Meanwhile, calcium consumption kinetics, transmission electron microscopy and selected area electron diffraction indicated that (QPX)5, C-tail and (QPX)3 had similar inhibitory effects on the spontaneous calcium consumption and the morphology of their nucleation products were alike, while QP5 had a greater inhibitory effect than them and induced elongated plate-like crystals. X-Ray diffraction further showed that both C-tail and (QPX)3 had greater potential in improving the apatite crystal orientation degree. In conclusion, (QPX)5 was the major adsorption region, both (QPX)5 and C-tail inhibited the nucleation, and C-tail contributed more to improve the HAP orientation degree, so QP5 could exert a significant remineralization effect. By reducing two repeats, (QPX)3 showed higher hydropathicity than (QPX)5 and achieved higher binding affinity, and it was more potential in improving the HAP orientation degree with lower economic cost.

Entropy-Enthalpy Compensation in Peptide Adsorption on Solid Surfaces: Dependence on Surface Hydration

Although protein adsorption at the solid-water interface is of immense importance, understanding the crucial role of the water phase in mediating protein-surface interactions is lacking, particularly due to the lack of fundamental thermodynamic data. Herein, we have performed complicated free energy calculations and successfully extracted the entropy and enthalpy changes of molecular adsorption on solids. Using the gold and graphene as the surface models with distinct affinities to the water phase, we successfully unravel the sharply opposite manners of entropy-enthalpy compensation in driving water and tripeptide adsorptions on two surfaces. Though the thermodynamic features of water adsorption on surface are enthalpically dominated based on the positions of free energy barriers and minima, the favorable entropy term significantly decreases the free energy barrier and further stabilizes the adsorbate at the adsorption site on the graphene surface. For the peptide, the shape of the adsorption free energy profile is jointly determined by the enthalpy and entropy changes, which, however, alternatively act the driving force to promote the peptide adsorption on the Au surface and graphene surface. The distinct structural and dynamic properties of solid-liquid interfaces account for the special role of the interfacial water phase in regulating the competitive relationship between the entropy and enthalpy variations.

Molecular docking and molecular dynamics simulation studies on the adsorption/desorption behavior of bone morphogenetic protein-7 on the β-tricalcium phosphate surface

The adsorption/desorption behavior, and conformational and orientational changes of proteins on the surface of biomaterials are significant parameters for understanding how biomaterials perform their biological functions. In this study, for the first time, the interactions between BMP-7 and β-TCP (001) surface models with different ion-rich terminations (Ca-rich and P-rich) were investigated by molecular dynamics simulation (MD) and steered molecular dynamics simulation (SMD). The results indicated that BMP-7 preferentially interacts with both Ca-rich and P-rich β-TCP (001) surfaces at its wrist epitope residues with certain conformational changes, which led to more exposure of BMP-7 knuckle epitope residues to the environment and facilitation for binding to the type II receptor. Compared to the P-rich surface, it is speculated that the Ca-rich surface was more conducive to BMP-7 signal transduction since the upright orientation of the protein adsorption would lead to smaller hindrance for receptor binding. This study provided more atomistic and molecular information for better understanding the process of Ca-P surfaces affecting BMP-7 biological properties and further interpreted the osteoinductive mechanism from the perspective of growth factor adsorption. Moreover, the docking screening method adopted in this study is of guiding significance to the design and development of bioactive materials.

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.

Pathways for the formation of ice polymorphs from water predicted by a metadynamics method

The mechanism of how ice crystal form has been extensively studied by many researchers but remains an open question. Molecular dynamics (MD) simulations are a useful tool for investigating the molecular-scale mechanism of crystal formation. However, the timescale of phenomena that can be analyzed by MD simulations is typically restricted to microseconds or less, which is far too short to explore ice crystal formation that occurs in real systems. In this study, a metadynamics (MTD) method was adopted to overcome this timescale limitation of MD simulations. An MD simulation combined with the MTD method, in which two discrete oxygen–oxygen radial distribution functions represented by Gaussian window functions were used as collective variables, successfully reproduced the formation of several different ice crystals when the Gaussian window functions were set at appropriate oxygen–oxygen distances: cubic ice, stacking disordered ice consisting of cubic ice and hexagonal ice, high-pressure ice VII, layered ice with an ice VII structure, and layered ice with an unknown structure. The free-energy landscape generated by the MTD method suggests that the formation of each ice crystal occurred via high-density water with a similar structure to the formed ice crystal. The present method can be used not only to study the mechanism of crystal formation but also to search for new crystals in real systems.

Impact of Glutamate Carboxylation in the Adsorption of the α-1 Domain of Osteocalcin to Hydroxyapatite and Titania

One proposed mechanism of implant fouling is attributed to the nonspecific adsorption of non-collagenous bone matrix proteins (NCPs) onto a newly implanted interface. With the goal of capturing the fundamental mechanistic and thermodynamic forces that govern changes in these NCP recognition domains as a function of γ-carboxyglutamic acid (Gla) post-translational modification and surface chemistry, we probe the adsorption process of the most commonly occurring NCP, osteocalcin, onto a mineral and metal oxide surface. Here, we apply two enhanced sampling methods to independently probe the effects of post-translational modification and peptide structure on adsorption. First, well-tempered metadynamics was used to capture the binding of acetyl and N-methylamide capped glutamic acid and Gla single amino acids onto crystalline hydroxyapatite and titania model surfaces at physiological pH. Following this, parallel tempering metadynamics in the well-tempered ensemble (PTMetaD-WTE) was used to study adsorption of the α-1 domain of osteocalcin onto hydroxyapatite and titania. Simulations were performed for the α-1 domain of osteocalcin in both its fully decarboxylated (dOC) and fully carboxylated (OC) form. Our simulations find that increased charge density due to carboxylation results in increased interactions at the interface, and stronger adsorption of the single amino acids to both surfaces. Interestingly, the role of Gla in promoting compact and helical structure in the α-1 domain resulted in disparate binding modes at the two surfaces, which is attributed to differences in interfacial water behavior. Overall, this work provides a benchmark for understanding the mechanisms that drive adsorption of Gla-containing mineralizing proteins onto different surface chemistries.

Comparative Study on Factors Governing Binding Mechanisms in Polylactic Acid-Hydroxyapatite and Polyethylene-Hydroxyapatite Systems via Molecular Dynamics Simulations

Binding mechanisms in polylactic acid-hydroxyapatite (PLA-HAp) and polyethylene-hydroxyapatite (PE-HAp) systems are comparatively elucidated on HAp (110) surfaces in unprecedented detail using molecular dynamics simulations conducted with the systematically varying number of monomers (N) between 10 and 400 at 310 K (NVT). Although PE seems to gradually cover the HAp surface more effectively compared to PLA, evident from the corresponding radius of gyration and occupied area values, the interface density and total binding energy in PLA-HAp systems is higher compared to those of PE-HAp systems. It is shown that a linear relationship between the binding energy and the surface area occupied by the monomer exists, consistent with our finding that binding energy converges to a limiting value with respect to monomer size on a constant surface area. The major constituent of the total binding energy is, rather surprisingly, shown to be the energy change in the bulk structure in HAp upon interaction; the next most important contributor is found to be the energy corresponding to surface-polymer interactions. The interplay between mainly these two contributors, acting in different fashions in two systems investigated here, seems to control the total binding energies. Increasing monomer size N initially results in enhanced densification of the interface in the HAp-PLA system up until N ≈ 200 with the positioning of mainly ═O units of PLA onto the HAp surface, consistent with the increasing Ca-O coordination numbers. Further increases in PLA size (N > 200) result in decreasing intensities of the peaks in the concentration profile consistent with the decreasing surface-polymer interaction energies while increased stabilization of the energy of the bulk is pronounced in this region. On the other hand, increasing N leads to a constantly increasing concentration at the interface in PE-HAp systems; -H atoms of the PE chain are positioned closer to the HAp surface than are -C atoms. These changes are coupled with increasing surface-polymer interaction energies in PE-HAp complexes, while slight destabilization in the energy of the bulk is observed for N > 100. A detailed examination of binding mechanisms in these technologically important systems as presented here is essential in material discovery; this valuable information, that will not be available from experiments can be attained through molecular simulations. The current study, to the best of our knowledge, comprises one of the first steps in achieving this goal for PLA/PE-HAp systems.

Constructing an Antibiofouling and Mineralizing Bioactive Tooth Surface to Protect against Decay and Promote Self-Healing

Numerous methods have been investigated to manage dental caries, one of the top three diseases threatening human health as reported by the World Health Organization. An innovative strategy was proposed to prevent dental caries and achieve self-healing of the decayed tooth, and a novel bioactive peptide was designed and synthesized to construct an antibiofouling and mineralizing dual-bioactive tooth surface. Compared to its original endogenous peptide, the synthesized bioactive peptide showed statistically significantly higher binding affinity to the tooth surface, stronger suppression of demineralization, and a certain promotion of tooth remineralization. The abilities of the peptide to inhibit Streptococcus mutans (S. mutans) biofilm formation and S. mutans adhesion on the tooth surface were not affected after synthesis. Biocompatibility tests revealed the safety of the synthesized bioactive peptide. Interaction mechanisms between the synthesized bioactive peptide and tooth surface were also explained by molecular dynamic simulation analysis. In summary, the synthesized bioactive peptide could be applied safely to prevent dental caries and effectively induce in situ self-healing remineralization for treatment of the decayed tooth.

Anisotropy in Stable Conformations of Hydroxylate Ions between the {001} and {110} Planes of TiO2 Rutile Crystals for Glycolate, Lactate, and 2-Hydroxybutyrate Ions Studied by Metadynamics Method

Control over TiO2 rutile crystal growth and morphology using additives is essential for the development of functional materials. Computer simulation studies on the thermodynamically stable conformations of additives at the surfaces of rutile crystals contribute to understanding the mechanisms underlying this control. In this study, a metadynamics method was combined with molecular dynamics simulations to investigate the thermodynamically stable conformations of glycolate, lactate, and 2-hydroxybutyrate ions at the {001} and {110} planes of rutile crystals. Two simple atom-atom distances were selected as collective variables for the metadynamics method. At the {001} plane, a conformation in which the COO- group was oriented toward the surface was found to be the most stable for the lactate and 2-hydroxybutyrate ions, whereas a conformation in which the COO- group was oriented toward water was the most stable for the glycolate ion. At the {110} plane, a conformation in which the COO- group was oriented toward the surface was the most stable for all three hydroxylate ions, and a second most stable conformation was also observed for the lactate ion at positions close to the {110} plane. For all three hydroxylate ions (α-hydroxycarboxylate ions), the stability of the most stable conformation was higher for the {110} plane than for the {001} plane. At both planes, the stability of the most stable conformation was highest for the 2-hydroxybutyrate ion and lowest for the glycolate ion. Supposing that all three hydroxylate ions serve to decrease the surface free energy at the rutile surface and that a more stable conformation at the rutile surface leads to a greater decrease in the surface free energy, the present results partially explain experimentally observed differences in the changes in growth rate and morphology of rutile crystals in the presence of glycolic, lactic, and 2-hydroxybutyric acids.

Molecular Driving Forces in Peptide Adsorption to Metal Oxide Surfaces

Molecular recognition between peptides and metal oxide surfaces is a fundamental process in biomineralization, self-assembly, and biocompatibility. Yet, the underlying driving forces and dominant mechanisms remain unclear, bringing obstacles to understand and control this process. To elucidate the mechanism of peptide/surface recognition, specifically the role of serine phosphorylation, we employed molecular dynamics simulation and metadynamics-enhanced sampling to study five artificial peptides, DDD, DSS, DpSpS, DpSpSGKK, and DpSKGpSK, interacting with two surfaces: rutile TiO₂ and quartz SiO₂. On both surfaces, we observe that phosphorylation increases the binding energy. However, the interfacial peptide conformation reveals a distinct binding mechanism on each surface. We also study the impact of peptide sequence to binding free energy and interfacial conformation on both surfaces, specifically the impact on the behavior of phosphorylated serine. Finally, the results are discussed in context of prior studies investigating the role of serine phosphorylation in peptide binding to silica.

Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides

The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.

Asymmetric Synthesis of Griffipavixanthone Employing a Chiral Phosphoric Acid-Catalyzed Cycloaddition

Asymmetric synthesis of the biologically active xanthone dimer griffipavixanthone is reported along with its absolute stereochemistry determination. Synthesis of the natural product is accomplished via dimerization of a p-quinone methide using a chiral phosphoric acid catalyst to afford a protected precursor in excellent diastereo- and enantioselectivity. Mechanistic studies, including an unbiased computational investigation of chiral ion-pairs using parallel tempering, were performed in order to probe the mode of asymmetric induction.

Molecular dynamics simulations of adsorption and desorption of bone morphogenetic protein-2 on textured hydroxyapatite surfaces

Interactions between bone morphogenetic protein-2 (BMP-2) and biomaterial surfaces are of great significance in the fields of regenerative medicine and bone tissue engineering. In this work, the adsorption and desorption behaviors of BMP-2 on a series of nano-textured hydroxyapatite (HAP) surfaces were systematically investigated by combined molecular dynamic (MD) simulations and steered molecular dynamic (SMD) simulations. The textured HAP surfaces exhibited nanostructured topographies and played a critical role in the mediation of dynamic behaviors of BMP-2. Compared to the HAP-flat model, the HAP-1:1 group (means ridge vs groove = 1:1) showed the excellent ability to capture BMP-2, less conformation change of BMP-2 molecule, and high cysteine-knot stability during the adsorption and desorption processes. These findings suggest that nano-textured HAP surfaces are more capable of loading BMP-2 molecules, and most importantly, they can help maintain a higher biological activity of BMP-2 cargos. In the present study, for the first time, we have deeply clarified the adsorption and desorption dynamics of BMP-2 on various nano-textured HAP surfaces at the atomic level, which can provide significant guidelines for the future design of BMP-2-based tissue engineering implants/scaffolds. STATEMENT OF SIGNIFICANCE: By using combined molecular dynamic (MD) simulations and steered molecular dynamic (SMD) simulations, the adsorption and desorption dynamics of bone morphogenetic protein-2 (BMP-2) dimer on a series of nano-textured hydroxyapatite (HAP) surfaces at the atomic level were presented in details for the first time. We have proved that the HAP-1:1 model (means ridge vs groove = 1:1) possessed excellent ability to capture BMP-2, less conformation change, and high cysteine-knot stability. As a result, the nano-textured topography of HAP-1:1 could maintain a relatively high biological activity of BMP-2 cargos. This work could provide theoretical guidelines for the design of BMP-2-based implants/scaffolds for bone tissue engineering.

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.

Origin of gypsum growth habit difference as revealed by molecular conformations of surface-bound citrate and tartrate

Correlation of the microscopic gypsum–organic interfacial structural information with the macroscopic crystal morphology difference induced by different organic acids.

Molecular Modelling of Peptide-Based Materials for Biomedical Applications

The molecular-level interactions between peptides and medically-relevant biomaterials, including nanoparticles, have the potential to advance technologies aimed at improving performance for medical applications including tissue implants and regenerative medicine. Peptides can possess materials-selective non-covalent adsorption properties, which in this instance can be exploited to enhance the biocompatibility and possible multi-functionality of medical implant materials. However, at present, their successful implementation in medical applications is largely on a trial-and-error basis, in part because a deep comprehension of general structure/function relationships at these interfaces is currently lacking. Molecular simulation approaches can complement experimental characterisation techniques and provide a wealth of relevant details at the atomic scale. In this Chapter, progress and prospects for advancing peptide-mediated medical implant surface treatments via molecular simulation is summarised for two of the most widely-found medical implant interfaces, titania and hydroxyapatite.

Identification of Specific Hydroxyapatite {001} Binding Heptapeptide by Phage Display and Its Nucleation Effect

With recent developments of molecular biomimetics that combine genetic engineering and nanotechnology, peptides can be genetically engineered to bind specifically to inorganic components and execute the task of collagen matrix proteins. In this study, using biogenous tooth enamel as binding substrate, we identified a new heptapeptide (enamel high-affinity binding peptide, EHBP) from linear 7-mer peptide phage display library. Through the output/input affinity test, it was found that EHBP has the highest affinity to enamel with an output/input ratio of 14.814 × 10-7, while a random peptide (RP) displayed much lower output/input ratio of 0.00035 × 10-7. This binding affinity was also verified by confocal laser scanning microscopy (CLSM) analysis. It was found that EHBP absorbing onto the enamel surface exhibits highest normalized fluorescence intensity (5.6 ± 1.2), comparing to the intensity of EHBP to enamel longitudinal section (1.5 ± 0.9) (p < 0.05) as well as to the intensity of a low-affinity binding peptide (ELBP) to enamel (1.5 ± 0.5) (p < 0.05). Transmission electron microscopy (TEM), Attenuated total Reflection-Fourier transform infrared spectroscopy (ATR-FTIR), and X-ray Diffraction (XRD) studies further confirmed that crystallized hydroxyapatite were precipitated in the mineralization solution containing EHBP. To better understand the nucleation effect of EHBP, EHBP was further investigated on its interaction with calcium phosphate clusters through in vitro mineralization model. The calcium and phosphate ion consumption as well as zeta potential survey revealed that EHBP might previously adsorb to phosphate (PO₄3-) groups and then initiate the precipitation of calcium and phosphate groups. This study not only proved the electrostatic interaction of phosphate group and the genetically engineering solid-binding peptide, but also provided a novel nucleation motif for potential applications in guided hard tissue biomineralization and regeneration.