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

Human collagen sequence polypeptides mediated biomineralization and its molecular mechanism

Biotechnology provides alternatives for regenerative medicine with more controllable functions. Herein, the polypeptides encoded with human collagen I amino-acid sequences were studied for the first time to modulate biomimetic hydroxyapatite (HAP). With a length of 50-100 nm and a width of 20-30 nm, the HAP crystal formed was plate-like. The interaction of the human collagen sequence polypeptide on the (001), (100), and (211) crystal faces of HAP crystal had been studied using Molecular Dynamics (MD) simulations, respectively. Based on MD simulations, van der Waals forces and hydrogen bonds are the main interactions between polypeptides and HAP through the -NH2, -CH2-, -OH, and -COOH, respectively. According to the calculated results, der Waals forces might be the main interaction. The human collagen sequence polypeptides exhibited the highest adsorption energy on the (001) plane of HAP, significantly higher than any of the adsorption energy on the (100) and (211) planes. Therefore, the growth of the (001) would be inhibited, which kept accurate with the result of images from the Transmission Electron Microscope (TEM). Study results provide a basis for rational designing of peptides with human collagen sequences to regenerate hard tissues.

Bridging Nature and Engineering: Protein-Derived Materials for Bio-Inspired Applications

The sophisticated, elegant protein-polymers designed by nature can serve as inspiration to redesign and biomanufacture protein-based materials using synthetic biology. Historically, petro-based polymeric materials have dominated industrial activities, consequently transforming our way of living. While this benefits humans, the fabrication and disposal of these materials causes environmental sustainability challenges. Fortunately, protein-based biopolymers can compete with and potentially surpass the performance of petro-based polymers because they can be biologically produced and degraded in an environmentally friendly fashion. This paper reviews four groups of protein-based polymers, including fibrous proteins (collagen, silk fibroin, fibrillin, and keratin), elastomeric proteins (elastin, resilin, and wheat glutenin), adhesive/matrix proteins (spongin and conchiolin), and cyanophycin. We discuss the connection between protein sequence, structure, function, and biomimetic applications. Protein engineering techniques, such as directed evolution and rational design, can be used to improve the functionality of natural protein-based materials. For example, the inclusion of specific protein domains, particularly those observed in structural proteins, such as silk and collagen, enables the creation of novel biomimetic materials with exceptional mechanical properties and adaptability. This review also discusses recent advancements in the production and application of new protein-based materials through the approach of synthetic biology combined biomimetics, providing insight for future research and development of cutting-edge bio-inspired products. Protein-based polymers that utilize nature's designs as a base, then modified by advancements at the intersection of biology and engineering, may provide mankind with more sustainable products.

The impact of chemical properties of the solid-liquid-adsorbate interfaces on the entropy-enthalpy compensation involved in adsorption

Despite extensive studies on the thermodynamic mechanism governing molecular adsorption at the solid-water interface, a comprehensive understanding of the crucial role of interface properties in mediating the entropy-enthalpy compensation during adsorption is lacking, particularly at a quantitative level. Herein, we employed two types of surface models (hydroxyapatite and graphene) along with a series of amino acids to successfully elucidate how distinct interfacial features dictate the delicate balance between entropy and enthalpy variations. The adsorption of all amino acids on the hydroxyapatite surface is an enthalpy-dominated process, where the water-induced enthalpic component of the free energy and the surface-adsorbate electrostatic interaction term alternatively act as the driving force for adsorption in different regions of the surface. Although favorable interactions are observed between amino acids and the graphene surface, the entropy-enthalpy compensation exhibits dependence on the molecular size of the adsorbates. For small amino acids, favorable enthalpy changes predominantly determine their adsorption behavior; however, larger amino acids tend to bind more tightly with the graphene surface, which is thermodynamically dominated by the entropy variations despite the structural characteristics of amino acids. This study reveals specific entropy-enthalpy mechanisms underlying amino acid adsorption at the solid-liquid interface, providing guidance for surface design and synthesis of new biomolecules.

Osteocalcin: Promoter or Inhibitor of Hydroxyapatite Growth?

Osteocalcin is the most abundant noncollagenous bone protein and the functions in bone remineralization as well as in inhibition of bone growth have remained unclear. In this contribution, we explain the dual role of osteocalcin in the nucleation of new calcium phosphate during bone remodeling and in the inhibition of hydroxyapatite crystal growth at the molecular scale. The mechanism was derived using pH-resolved all-atom models for the protein, phosphate species, and hydroxyapatite, along with molecular dynamics simulations and experimental and clinical observations. Osteocalcin binds to (hkl) hydroxyapatite surfaces through multiple residues, identified in this work, and the fingerprint of binding residues varies as a function of the (hkl) crystal facet and pH value. On balance, the affinity of osteocalcin to hydroxyapatite slows down crystal growth. The unique tricalcium γ-carboxylglutamic acid (Gla) domain hereby rarely adsorbs to hydroxyapatite surfaces and faces instead toward the solution. The Gla domain enables prenucleation of calcium phosphate for new bone formation at a slightly acidic pH of 5. The growth of prenucleation clusters of calcium phosphate continues upon increase in pH value from 5 to 7 and is much less favorable, or not observed, on the native osteocalcin structure at and above neutral pH values of 7. The results provide mechanistic insight into the early stages of bone remodeling from the molecular scale, help inform mutations of osteocalcin to modify binding to apatites, support drug design, and guide toward potential cures for osteoporosis and hyperosteogeny.

Optimized biomimetic minerals maintain activity of mRNA complexes after long term storage

mRNA therapeutics can be readily designed, manufactured, and brought to scale, as demonstrated by widespread global vaccination against COVID-19. However, mRNA therapies require cold chain shipment and storage from manufacturing to administration, which may limit them to affluent communities. This problem could be addressed by mimicking the known ability of mineralized fossils to durably stabilize nucleic acids under extreme conditions. We synthesized and screened 40 calcium-phosphate minerals for their ability to store and maintain the activity of lyophilized mRNA complexes. The optimal mineral formulation incorporated mRNA complexes with high efficiency (77 %), and increased mRNA transfection efficiency by 5.6-fold. Lyophilized mRNA complexes stored with the optimized mineral formulation for 6 months at 25 °C were 3.2-fold more active than those stored with state-of-the-art excipients, but without a mineral. mRNA complexes stored with minerals at room temperature did not decline in transfection efficacy from 3 days to 6 months of storage, indicating that minerals can durably maintain activity of therapeutic mRNA complexes without cold chain storage. STATEMENT OF SIGNIFICANCE: Therapeutic mRNA, such as mRNA COVID-19 vaccines, require extensive cold chain storage that limits their general application. This work screened a library of minerals to maintain the activity of mRNA complexes with freeze-drying. The optimized mineral was able to maintain mRNA activity up to 6 months of storage at room temperature outperforming current methods of freeze-drying therapeutic mRNA complexes.

Dentine tubule occlusion effect of hydrolyzed casein in a bioactive glass-based dental desensitizing gel

OBJECTIVES

The effectiveness of three different groups of polyethylene glycol (PEG)-based gels containing powders on dentin hypersensitivity (DH) treatment were assessed and compared with Actimins® as commercial reference group.

METHODS

Hydroxyapatite nanorods (nHA) and sol-gel-derived 45S5 bioglass (SGD 45S5) powders were synthesized through hydrothermal and sol-gel methods, respectively. First, 25 demineralized dentin disks were divided into five groups. Then, the prepared gels based on 45S5 bioglass with and without hydrolyzed casein (HC) as experimental, nHA gel and Actimins® as positive and commercial reference groups were applied twice a day on disks by a micro applicator. To mimic the oral environment, treated disks were immersed in artificial saliva in a water bath at 37 °C for 7 days. However, in the negative control group, no agent was applied on the samples. FE-SEM, EDS, AFM, and XRD were performed to assess tubule occlusion. One-way ANOVA test was used for statistical analysis and p*<0.05 was set as the significance level.

RESULTS

The nHA with an average aspect ratio of 2.77 and the SGD 45S5 powders with a polygonal morphology and the average size of 48.64±11.38 µm were synthesized. After treatment, tubule occlusion in HC-SGD 45S5 and nHA gels were shown to be higher than other groups. The root mean square roughness (Rrms) of the above-mentioned gels showed to be 121.54±9.25 nm, and 312.6 ± 9 nm, respectively.

CONCLUSION

The nHA containing group exhibited the highest tubule occlusion efficiency (i.e., tubule diameter of 0.92±0.32 µm) with a superior mineral precipitation. HC as a novel material demonstrates to be potentially beneficial in DH treatment.

CLINICAL SIGNIFICANCE

DH as a common issue may be reduced or eliminated by occlusion of patent dentinal tubules. There are various types of desensitizing agents capable of controlling the DH by the occlusion of patent dentinal tubules. The desensitizing gels developed in this study showed to be promising for clinical and home-use applications.

Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale

The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed.

Regulation of recombinant humanized collagen on HAP growth and its molecule simulation

Hydroxyapatite (HAP) in natural bone is formed under the regulation of natural collagen I. Here, we report how recombinant humanized collagen I (rhCol I) regulates the growth of HAP nanocrystals in a long belt shape 100-150 nm in width and 200-300 nm in length. MD simulation results showed that the interactions between rhCol I and the (001), (100), and (211) planes of HAP mainly contributed to the electrostatic force and van der Waals forces via COO⋯Ca, -NH⋯Ca, CH⋯OPO3, and NH⋯OPO3 bonds, respectively. On the (001) plane, the interaction between -COO- and Ca was stronger than on the (100) and (211) planes, resulting in a large electrostatic force, which inhibited the growth of the (001) plane. The lowest energy of adsorption to the (211) plane resulted in the preferential growth of the (211) plane due to the weakest interaction with rhCol I. The detailed correlation between HAP and rhCol I could explain HAP growth under regulation by rhCol I. This study provides a reference for the bio-application of recombinant collagen.

Insight into the Binding Mechanisms of Quartz-Selective Peptides: Toward Greener Flotation Processes

Mining practices, chiefly froth flotation, are being critically reassessed to replace their use of biohazardous chemical reagents in favor of biofriendly alternatives as a path toward green processes. In this regard, this study aimed at evaluating the interactions of peptides, as potential floatation collectors, with quartz using phage display and molecular dynamics (MD) simulations. Quartz-selective peptide sequences were initially identified by phage display at pH = 9 and further modeled by a robust simulation scheme combining classical MD, replica exchange MD, and steered MD calculations. Our residue-specific analyses of the peptides revealed that positively charged arginine and lysine residues were favorably attracted by the quartz surface at basic pH. The negatively charged residues at pH 9 (i.e., aspartic acid and glutamic acid) further showed affinity toward the quartz surface through electrostatic interactions with the positively charged surface-bound Na⁺ ions. The best-binding heptapeptide combinations, however, contained both positively and negatively charged residues in their composition. The flexibility of peptide chains was also shown to directly affect the adsorption behavior of the peptide. While attractive intrapeptide interactions were dominated by a weak peptide-quartz binding, the repulsive self-interactions in the peptides improved the binding propensity to the quartz surface. Our results showed that MD simulations are fully capable of revealing mechanistic details of peptide adsorption to inorganic surfaces and are an invaluable tool to accelerate the rational design of peptide sequences for mineral processing applications.

Biogenic Hydroxyapatite Obtained from Bone Wastes Using CO2-Assisted Pyrolysis and Its Interaction with Glyphosate: A Computational and Experimental Study

In this work, biogenic hydroxyapatite (BHap) obtained from cattle bone waste is proposed as an adsorbent of this dangerous pollutant. Density functional theory (DFT) and calorimetric studies were developed to study the interaction between BHap and glyphosate (GLY). A strong interaction was found in the experiments through the measurement of immersion enthalpy, confirmed by the exothermic chemisorption obtained with DFT calculations. These results suggest that hydroxyapatite is a promising adsorbent material for GLY adsorption in aqueous solutions. In addition, it was determined that the GLY-hydroxyapatite interaction is greater than the water-hydroxyapatite interaction, which favors the GLY adsorption into this material.

Amyloid-like amelogenin nanoribbons template mineralization via a low-energy interface of ion binding sites

Protein scaffolds direct the organization of amorphous precursors that transform into mineralized tissues, but the templating mechanism remains elusive. Motivated by models for the biomineralization of tooth enamel, wherein amyloid-like amelogenin nanoribbons guide the mineralization of apatite filaments, we investigated the impact of nanoribbon structure, sequence, and chemistry on amorphous calcium phosphate (ACP) nucleation. Using full-length human amelogenin and peptide analogs with an amyloid-like domain, films of β-sheet nanoribbons were self-assembled on graphite and characterized by in situ atomic force microscopy and molecular dynamics simulations. All sequences substantially reduce nucleation barriers for ACP by creating low-energy interfaces, while phosphoserines along the length of the nanoribbons dramatically enhance kinetic factors associated with ion binding. Furthermore, the distribution of negatively charged residues along the nanoribbons presents a potential match to the Ca–Ca distances of the multi-ion complexes that constitute ACP. These findings show that amyloid-like amelogenin nanoribbons provide potent scaffolds for ACP mineralization by presenting energetically and stereochemically favorable templates of calcium phosphate ion binding and suggest enhanced surface wetting toward calcium phosphates in general.

Protein-Based Hydrogels: Promising Materials for Tissue Engineering

The successful design of a hydrogel for tissue engineering requires a profound understanding of its constituents' structural and molecular properties, as well as the proper selection of components. If the engineered processes are in line with the procedures that natural materials undergo to achieve the best network structure necessary for the formation of the hydrogel with desired properties, the failure rate of tissue engineering projects will be significantly reduced. In this review, we examine the behavior of proteins as an essential and effective component of hydrogels, and describe the factors that can enhance the protein-based hydrogels' structure. Furthermore, we outline the fabrication route of protein-based hydrogels from protein microstructure and the selection of appropriate materials according to recent research to growth factors, crucial members of the protein family, and their delivery approaches. Finally, the unmet needs and current challenges in developing the ideal biomaterials for protein-based hydrogels are discussed, and emerging strategies in this area are highlighted.