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

Computational Biomaterials: Computational Simulations for Biomedicine

With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.

Frontiers of Hydroxyapatite Composites in Bionic Bone Tissue Engineering

Bone defects caused by various factors may cause morphological and functional disorders that can seriously affect patient's quality of life. Autologous bone grafting is morbid, involves numerous complications, and provides limited volume at donor site. Hence, tissue-engineered bone is a better alternative for repair of bone defects and for promoting a patient's functional recovery. Besides good biocompatibility, scaffolding materials represented by hydroxyapatite (HA) composites in tissue-engineered bone also have strong ability to guide bone regeneration. The development of manufacturing technology and advances in material science have made HA composite scaffolding more closely related to the composition and mechanical properties of natural bone. The surface morphology and pore diameter of the scaffold material are more important for cell proliferation, differentiation, and nutrient exchange. The degradation rate of the composite scaffold should match the rate of osteogenesis, and the loading of cells/cytokine is beneficial to promote the formation of new bone. In conclusion, there is no doubt that a breakthrough has been made in composition, mechanical properties, and degradation of HA composites. Biomimetic tissue-engineered bone based on vascularization and innervation show a promising future.

Engineered cells along with smart scaffolds: critical factors for improving tissue engineering approaches

In this review, gene delivery and its applications are discussed in tissue engineering (TE); also, new techniques such as the CRISPR-Cas9 system, synthetics biology and molecular dynamics simulation to improve the efficiency of the scaffolds have been studied. CRISPR-Cas9 is expected to make significant advances in TE in the future. The fundamentals of synthetic biology have developed powerful and flexible methods for programming cells via artificial genetic circuits. The combination of regenerative medicine and artificial biology allows the engineering of cells and organisms for use in TE, biomaterials, bioprocessing and scaffold development. The dynamics of protein adsorption at the scaffold surface at the atomic level can provide valuable guidelines for the future design of TE scaffolds /implants.

Effects of Substitution Ratios of Zinc-Substituted Hydroxyapatite on Adsorption and Desorption Behaviors of Bone Morphogenetic Protein-2

Understanding interactions between bone morphogenetic proteins (BMPs) and biomaterials is of great significance in preserving the structure and bioactivity of BMPs when utilized in clinical applications. Currently, bone morphogenetic protein-2 (BMP-2) is one of the most important growth factors in bone tissue engineering; however, atomistic interactions between BMP-2 and zinc-substituted hydroxyapatite (Zn-HAP, commonly used in artificial bone implants) have not been well clarified until now. Thus, in this work, the interaction energies, binding/debinding states, and molecular structures of BMP-2 upon a series of Zn-HAP surfaces (Zn-HAPs, 1 at%, 2.5 at%, 5 at%, and 10 at% substitution) were investigated by hybrid molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. Meanwhile, cellular studies including alkaline phosphatase (ALP) activity and reverse transcription-polymerase chain reaction (RT-PCR) assay were performed to verify the theoretical modeling findings. It was found that, compared to pure HAP, Zn-HAPs exhibited a higher binding affinity of BMP-2 at the adsorption process; meanwhile, the detachment of BMP-2 upon Zn-HAPs was more difficult at the desorption process. In addition, molecular structures of BMP-2 could be well stabilized upon Zn-HAPs, especially for Zn10-HAP (with a 10 at% substitution), which showed both the higher stability of cystine-knots and less change in the secondary structures of BMP-2 than those upon HAP. Cellular studies confirmed that higher ALP activity and osteogenic marker gene expression were achieved upon BMP-2/Zn-HAPs than those upon BMP-2/HAP. These findings verified that Zn-HAPs favor the adsorption of BMP-2 and leverage the bioactivity of BMP-2. Together, this work clarified the interaction mechanisms between BMP-2 and Zn-HAPs at the atom level, which could provide new molecular-level insights into the design of BMP-2-loaded biomaterials for bone tissue engineering.

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

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

Nanoscale Topographical Effects on the Adsorption Behavior of Bone Morphogenetic Protein-2 on Graphite

The interaction between bone morphogenetic protein-2 (BMP-2) and the surface of biomaterials is essential for the restoration of bone and cartilage tissue, inducing cellular differentiation and proliferation. The properties of the surface, including topology features, regulate the conformation and bioactivity of the protein. In this research, we investigated the influence of nanopatterned surfaces on the interaction of a homodimer BMP-2 with graphite material by combining molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The graphite substrates were patterned as flat, linear grating, square, and circular profiles in combination with BMP-2 conformation in the side-on configuration. Ramachandran plots for the wrist and knuckle epitopes indicated no steric hindrances and provided binding sites to type I and type II receptors. Results showed two optimal patterns that increased protein adsorption of the lower monomer while preserving the secondary structure and leaving the upper monomer free to interact with the cells. Charged residues arginine and lysine and polar residues histidine and tyrosine were the main residues responsible for the strong interaction with the graphite surface. This research provides new molecular-level insights to further understand the mechanisms underlying protein adsorption on nanoscale patterned substrates.

An Atomistic Investigation of Adsorption of Bone Morphogenetic Protein-2 on Gold with Nanoscale Topographies

Nanoscale surface topographies mediated with biochemical cues influence the differentiation of stem cells into different lineages. This research focuses on the adsorption behavior of bone morphogenetic protein (BMP-2) on nanopatterned gold substrates, which can aid in the differentiation of bone and cartilage tissue constructs. The gold substrates were patterned as flat, pillar, linear grating, and linear-grating deep based, and the BMP-2 conformation in end-on configuration was studied over 20 ns. The linear grating deep substrate pattern had the highest adsorption energy of around 125 kJ/mol and maintained its radius of gyration of 18.5 Å, indicating a stable adsorption behavior. Secondary structures including α-helix and β-sheet displayed no denaturation, and thus, the bioavailability of the BMP-2, for the deep linear-grating pattern. Ramachandran plots for the wrist and knuckle epitopes indicated no steric hindrances and provided binding sites to type I and type II receptors. The deep linear-grating substrate had the highest number of contacts (88 atoms) within 5 Å of the gold substrate, indicating its preferred nanoscale pattern choice among the substrates considered. This research provides new insights into the atomistic adsorption of BMP-2 on nanoscale topographies of a gold substrate, with applications in biomedical implants and regenerative medicine.

Antimicrobial Peptides-Loaded Hydroxyapatite Microsphere With Different Hierarchical Structures for Enhanced Drug Loading, Sustained Release and Antibacterial Activity

Antimicrobial peptides (AMPs) have great potential for clinical treatment of bacterial infection due to the broad-spectrum and highly effective antibacterial activity. However, the easy degradation and inactivation in vivo has been a major obstacle for their application and an effective delivery system is demanding. The surface physicochemical properties of the carrier, including surface potential, surface polarity, pore structure and morphology, have exerted great effects on the adsorption and release behavior of AMPs. This study investigated the influence of micro/nano carriers with different hierarchical structures on the loading, release and biological behavior of AMPs. Three types of AMPs-loaded hydroxyapatite microspheres (HA/AMPs MSs) with different hierarchical structures (needle-like, rod-like, and flake-like) were developed, which was investigated by the surface morphology, chemical composition and surface potential in detail. The different hierarchical structures of hydroxyapatite microspheres (HA MSs) had noticeable impact on the loading and release behavior of AMPs, and the flake-like HA MSs with hierarchical structure showed the highest loading efficiency and long-lasting release over 9 days. Meanwhile, the stability of AMPs released from HA MSs was effectively maintained. Moreover, the antibacterial test indicated that the flake-like HA/AMPs MSs showed more sustained antibacterial properties among three composites. In view of the excellent biocompatibility and osteogenic property, high loading efficiency and the long-term release properties of HA MSs with hierarchical structure, the HA/AMPs MSs have a great potential in bone tissue engineering.

The regulating effect of trace elements Si, Zn and Sr on mineralization of gelatin-hydroxyapatite electrospun fiber

Biomineralization approaches have been increasingly adopted to synthesizing advanced materials with superior properties. Nevertheless, the potential influence of inorganic trace elements on the mineralization process of collagen has been rarely reported, despite of the significant progress achieved on exploiting the critical roles of organic polymers in regulating the collagen mineralization. To this aim, the potential roles of Si, Zn and Sr in regulating the mineralization of gelatin-hydroxyapatite (HA) composite fibers have been examined in this study. The results indicated that the incorporation of trace elements not only promoted the biomineralization of gelatin, but also led to drastic change in the mineralization behavior. In particular, the gelatin-SiHA sample showed uniform mineralization predominantly inside the fibers, with nucleation and growth directions along the c-axis of the gelatin fibers. On the contrary, the gelatin-HA sample showed nucleation outside the fibers and spherical mineral crystals on top of fibers, typical structure for heterogeneous nucleation. As the mineralization process proceeded, the gelatin-ZnHA and gelatin-SrHA samples evolved into having similar structure as the gelatin-SiHA sample, despite of showing totally different mineralization behaviors at early time. Overall, the incorporation of trace elements seemed to lower the nucleation barriers, led to a more homogeneous mineralization mode within the fiber region and formation of mineralized structures closer to those in natural bone. Moreover, mineralized samples with trace elements demonstrated improved adhesion and cytoskeleton organization of osteoblastic cells. Such finding would provide important insight for understanding the mineralization process and the optimal design of advanced biological materials.

Advances in Growth Factor Delivery for Bone Tissue Engineering

Shortcomings related to the treatment of bone diseases and consequent tissue regeneration such as transplants have been addressed to some extent by tissue engineering and regenerative medicine. Tissue engineering has promoted structures that can simulate the extracellular matrix and are capable of guiding natural bone repair using signaling molecules to promote osteoinduction and angiogenesis essential in the formation of new bone tissues. Although recent studies on developing novel growth factor delivery systems for bone repair have attracted great attention, taking into account the complexity of the extracellular matrix, scaffolding and growth factors should not be explored independently. Consequently, systems that combine both concepts have great potential to promote the effectiveness of bone regeneration methods. In this review, recent developments in bone regeneration that simultaneously consider scaffolding and growth factors are covered in detail. The main emphasis in this overview is on delivery strategies that employ polymer-based scaffolds for spatiotemporal-controlled delivery of both single and multiple growth factors in bone-regeneration approaches. From clinical applications to creating alternative structural materials, bone tissue engineering has been advancing constantly, and it is relevant to regularly update related topics.

HA-g-CS Implant and Moderate-intensity Exercise Stimulate Subchondral Bone Remodeling and Promote Repair of Osteochondral Defects in Mice

Background: Substantial evidence shows that crosstalk between cartilage and subchondral bone may play an important role in cartilage repair. Animal models have shown that hydroxyapatite-grafted-chitosan implant (HA-g-CS) and moderate-intensity exercise promote regeneration of osteochondral defects. However, no in vivo studies have demonstrated that these two factors may have a synergistic activity to facilitate subchondral bone remodeling in mice, thus supporting bone-cartilage repair. Questions: This study was to clarify whether HA-g-CS and moderate-intensity exercise might have a synergistic effect on facilitating (1) regeneration of osteochondral defects and (2) subchondral bone remodeling in a mouse model of osteochondral defects. Methods: Mouse models of osteochondral defects were created and divided into four groups. BC Group was subjected to no treatment, HC Group to HA-g-CS implantation into osteochondral defects, ME group to moderate-intensity treadmill running exercise, and HC+ME group to both HA-g-CS implantation and moderate-intensity exercise until sacrifice. Extent of subchondral bone remodeling at the injury site and subsequent cartilage repair were assessed at 4 weeks after surgery. Results: Compared with BC group, HC, ME and HC+ME groups showed more cartilage repair and thicker articular cartilage layers and HC+ME group acquired the best results. The extent of cartilage repair was correlated positively to bone formation activity at the injured site as verified by microCT and correlation analysis. Histology and immunofluorescence staining confirmed that bone remodeling activity was increased in HC and ME groups, and especially in HC+ME group. This bone formation process was accompanied by an increase in osteogenesis and chondrogenesis factors at the injury site which promoted cartilage repair. Conclusions: In a mouse model of osteochondral repair, HA-g-CS implant and moderate-intensity exercise may have a synergistic effect on improving osteochondral repair potentially through promotion of subchondral bone remodeling and generation of osteogenesis and chondrogenesis factors. Clinical Relevance: Combination of HA-g-CS implantation and moderate-intensity exercise may be considered potentially in clinic to promote osteochondral defect repair. Also, cartilage and subchondral bone forms a functional unit in an articular joint and subchondral bone may regulate cartilage repair by secreting growth factors in its remodeling process. However, a deeper insight into the exact role of HA-g-CS implantation and moderate-intensity exercise in promoting osteochondral repair in other animal models should be explored before they can be applied in clinic in the future.

Biomaterials Regulating Bone Hematoma for Osteogenesis

Blood coagulation in tissue healing not only prevents blood loss, but also forms a natural scaffold for tissue repair and regeneration. As blood clot formation is the initial and foremost phase upon bone injury, and the quality of blood clot (hematoma) orchestrates the following inflammatory and cellular processes as well as the subsequent callus formation and bone remodeling process. Inspired by the natural healing hematoma, tissue-engineered biomimic scaffold/hydrogels and blood prefabrication strategies attract significant interests in developing functional bone substitutes. The alteration of the fracture hematoma ca significantly accelerate or impair the overall bone healing process. This review summarizes the impact of biomaterials on blood coagulation and provides evidence on fibrin network structure, growth factors, and biomolecules that contribute to bone healing within the hematoma. The aim is to provide insights into the development of novel implant and bone biomaterials for enhanced osteogenesis. Advances in the understanding of biomaterial characteristics (e.g., morphology, chemistry, wettability, and protein adsorption) and their effect on hematoma properties are highlighted. Emphasizing the importance of the initial healing phase of the hematoma endows the design of advanced biomaterials with the desired regulatory properties for optimal coagulation and hematoma properties, thereby facilitating enhanced osteogenesis and ideal therapeutic effects.

Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design

Computationally driven engineering of proteins aims to allow them to withstand an extended range of conditions and to mediate modified or novel functions. Therefore, it is crucial to the biotechnological industry, to biomedicine and to afford new challenges in environmental sciences, such as biocatalysis for green chemistry and bioremediation. In order to achieve these goals, it is important to clarify molecular mechanisms underlying proteins stability and modulating their interactions. So far, much attention has been given to hydrophobic and polar packing interactions and stability of the protein core. In contrast, the role of electrostatics and, in particular, of surface interactions has received less attention. However, electrostatics plays a pivotal role along the whole life cycle of a protein, since early folding steps to maturation, and it is involved in the regulation of protein localization and interactions with other cellular or artificial molecules. Short- and long-range electrostatic interactions, together with other forces, provide essential guidance cues in molecular and macromolecular assembly. We report here on methods for computing protein electrostatics and for individual or comparative analysis able to sort proteins by electrostatic similarity. Then, we provide examples of electrostatic analysis and fingerprints in natural protein evolution and in biotechnological design, in fields as diverse as biocatalysis, antibody and nanobody engineering, drug design and delivery, molecular virology, nanotechnology and regenerative medicine.

Tailorable hierarchical structures of biomimetic hydroxyapatite micro/nano particles promoting endocytosis and osteogenic differentiation of stem cells

Hydroxyapatite (HA) micro/nano particles show great promise as artificial bone and dental substitutes, or drug carrier systems. However, the precise regulation of hydroxyapatite micro/nano particles with controllable physicochemical properties (such as hierarchical structure, particle size, potential and crystallinity) is still a challenge. Furthermore, the effects of different hierarchical structures on biological responses have been rarely reported. Herein, the HA particles with a precisely tailored micro/nano hierarchical structure have been developed using an elaborate biomimetic synthesis technology. Three representative particles, namely, micro/nano needle-like HA particles, micro/nano rod-like HA particles, and micro/nano flake-like HA particles, were featured to evaluate their biological responses to stem cells. The pore structure facilitated the adsorption of serum adhesive proteins, which together with the unique hierarchical architecture of micro/nano flake-like HA particles remarkably promoted the endocytosis efficiency in a concentration-dependent manner. The qRT-PCR together with RNA-seq and western blot analyses showed that micro/nano flake-like HA particles more significantly up-regulated the expression of genes and production of proteins related to osteogenic differentiation among the three particles through the activated ERK/MAPK signalling pathway. RNA-seq further revealed a complex mechanism of cell interface events, suggesting that the hierarchical architecture of HA particles is of crucial importance for the regulation of actin cytoskeleton involved in the modulation of cell adhesion which positively stimulated osteogenic differentiation of stem cells. Moreover, the endocytosis of particles into lysosomes resulted in an increase in the intracellular Ca²⁺ levels, which activated possible intracellular Ca²⁺-mediated signaling cascades (Ras/cAMP/Rap1/MAPK signaling pathways) related to osteogenic differentiation of stem cells. Our findings shed light on the effects of different hierarchical structures of HA particles on stem cell differentiation and contribute to the optimal design of implant materials.

In Silico Studies for Bacterystic Evaluation against Staphylococcus aureus of 2-Naphthoic Acid Analogues

Background:

Staphylococcus aureus is a gram-positive spherical bacterium commonly present in nasal fossae and in the skin of healthy people; however, in high quantities, it can lead to complications that compromise health. The pathologies involved include simple infections, such as folliculitis, acne, and delay in the process of wound healing, as well as serious infections in the CNS, meninges, lung, heart, and other areas.

Aim:

This research aims to propose a series of molecules derived from 2-naphthoic acid as a bioactive in the fight against S. aureus bacteria through in silico studies using molecular modeling tools.

Methods:

A virtual screening of analogues was done in consideration of the results that showed activity according to the prediction model performed in the KNIME Analytics Platform 3.6, violations of the Lipinski rule, absorption rate, cytotoxicity risks, energy of binder-receptor interaction through molecular docking, and the stability of the best profile ligands in the active site of the proteins used (PDB ID 4DXD and 4WVG).

Results:

Seven of the 48 analogues analyzed showed promising results for bactericidal action against S. aureus.

Conclusion:

It is possible to conclude that ten of the 48 compounds derived from 2-naphthoic acid presented activity based on the prediction model generated, of which seven presented no toxicity and up to one violation to the Lipinski rule.

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.

Optimizing Nanohydroxyapatite Nanocomposites for Bone Tissue Engineering

Bone tissue engineering involves the combined use of materials with functional properties to regenerate bone. Nanohydroxyapatite (nHA) can influence the behavior of cells. The functional and structural properties of nHA can be controlled during nanoparticle synthesis. This review defines the relationship between the attributes of nHA nanoparticles and their biological effects, focusing on biocompatibility, surface-area-to-volume ratio, bonding chemistry, and substrate functionality. The paper explores how these aspects have been applied in the development of scaffolds for the repair of damaged bone or regeneration of missing bone.

Methacrylate Coatings for Titanium Surfaces to Optimize Biocompatibility

Currently, there are more than 1.5 million knee and hip replacement procedures carried out in the United States. Implants have a 10-15-year lifespan with up to 30% of revision surgeries showing complications with osteomyelitis. Titanium and titanium alloys are the favored implant materials because they are lightweight and have high mechanical strength. However, this increased strength can be associated with decreased bone density around the implant, leading to implant loosening and failure. To avoid this, current strategies include plasma-spraying titanium surfaces and foaming titanium. Both techniques give the titanium a rough and irregular finish that improves biocompatibility. Recently, researchers have also sought to surface-conjugate proteins to titanium to induce osteointegration. Cell adhesion-promoting proteins can be conjugated to methacrylate groups and crosslinked using a variety of methods. Methacrylated proteins can be conjugated to titanium surfaces through atom transfer radical polymerization (ATRP). However, surface conjugation of proteins increases biocompatibility non-specifically to bone cells, adding to the risk of biofouling which may result in osteomyelitis that causes implant failure. In this work, we analyze the factors contributing to biofouling when coating titanium to improve biocompatibility, and design an experimental scheme to evaluate optimal coating parameters.

Orientation effects on the nanoscale adsorption behavior of bone morphogenetic protein-2 on hydrophilic silicon dioxide

Bone Morphogenetic Protein-2 (BMP-2) is a growth factor associated with different developmental functions in regenerative medicine and tissue engineering. Because of its favorable properties for the development of bone and cartilage tissue, BMP-2 promotes the biocompatibility of medical implants. In this research, molecular dynamics simulations were implemented to simulate the interaction of BMP-2 with a flat hydrophilic silicon dioxide substrate, an important biomaterial for medical applications. We considered the influence of four orthogonal protein orientations on the adsorption behavior. Results showed that arginine and lysine were the main residues to interact with the silicon dioxide substrate, directly adsorbing onto the surface and overcoming water layers. However, between these charged residues, we observed a preference for arginine to adsorb. Orientations with the α-helix loop closer to the surface at the beginning of the simulations had greater loss of secondary structure as compared to the other configurations. Among all the orientations, the end-on B configuration had favorable adsorption characteristics with a binding energy of 14 000 kJ mol⁻¹ and retention of 21.7% β-sheets as confirmed by the Ramachandran plots. This research provides new insights into the nanoscale interaction of BMP-2 and silicon dioxide substrate with applications in orthopedic implants and regenerative medicine.

Preferential binding of charged residues with hydrophilic silicon dioxide substrate during adsorption of BMP-2 in end-on B configuration.