Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate

Microbial-induced Synthesis of nano NiFe LDH for High-efficiency Oxygen Evolution

NiFe layered double hydroxide (LDH) currently are the most efficient catalysts for the oxygen evolution reaction (OER) in alkaline environments. However, the development of high-performance low cost OER electrocatalysts using straightforward strategies remains a significant challenge. In this study, we describe an innovative microbial mineralization-based method for in situ-induced preparation of NiFe LDH nanosheets loaded on nickel foam and demonstrate that this material serves as an efficient oxygen evolution electrocatalyst. In the microbial mineralization process, bacteria adhere to electrode materials and promote the surface nucleation of nanomaterials when metal ions are present. Specifically, our findings indicate that biomineralization accelerates the formation and regulation of NiFe LDH. The new electrocatalyst displays excellent OER performance, with a small overpotential of 220 mV at 10 mA cm-2 and a Tafel slope down to 38.6 mV dec-1 in alkaline solution. The remarkable OER performance of the microbial mineralization-derived electrocatalyst is attributed to the synergistic effect of NiFe LDH and a bacterial-specific surface area that contains multiple active sites. This study has uncovered a new approach for the assembly of NiFe LDH that relies on biomineralization to bring about morphological and structural modification of LDH nanosheets.

Nucleation Domains in Biomineralization: Biomolecular Sequence and Conformational Features

Biomolecules play a vital role in the regulation of biomineralization. However, the characteristics of practical nucleation domains are still sketchy. Herein, the effects of the representative biomolecular sequence and conformations on calcium phosphate (Ca-P) nucleation and mineralization are investigated. The results of computer simulations and experiments prove that the line in the arrangement of dual acidic/essential amino acids with a single interval (Bc (Basic) -N (Neutral) -Bc-N-Ac (Acidic)- NN-Ac-N) is most conducive to the nucleation. 2α-helix conformation can best induce Ca-P ion cluster formation and nucleation. "Ac- × × × -Bc" sequences with α-helix are found to be the features of efficient nucleation domains, in which process, molecular recognition plays a non-negligible role. It further indicates that the sequence determines the potential of nucleation/mineralization of biomolecules, and conformation determines the ability of that during functional execution. The findings will guide the synthesis of biomimetic mineralized materials with improved performance for bone repair.

Purification of Intramineral Peptides from Cuttlebones and In Vitro Activity in CaCO3 Biomineralization

Living organisms develop functional hard structures such as teeth, bones, and shells from calcium salts through mineralization for managing vital functions to sustain life. However, the exact mechanism or role of biomolecules such as proteins and peptides in the biomineralization process to form defect-free hierarchical structures in nature is poorly understood. In this study, we have extracted, purified, and characterized five major peptides (CBP1-CBP5) from the soluble organic materials (SOMs) of cuttlefish bone (CB) and used for the in vitro mineralization of calcium carbonate crystals. The SOMs induced nucleation of the calcite phase at low concentrations and the vaterite phase at high concentrations. The purified peptides nucleated calcite crystals and enhanced aggregation under laboratory conditions. Among five peptides, only CBP2 and CBP3 showed concentration-dependent nucleation, aggregation, and morphological changes of the calcite crystals within 12 h. Circular dichroism studies showed that the peptides CBP2 and CBP3 are in alpha helix and β-sheet conformation, respectively, in solution. CBP1 and CBP4 and CBP5 are in random coil and β-sheet conformation, respectively. In addition, the peptides showed different sizes in solution in the absence (∼27 nm, low aggregation) and presence (∼118 nm, high aggregation) of calcium ions. Aragonite crystals with needle-type morphologies were nucleated in the presence of Mg²⁺ ions in solution. Overall, exploring the activities of such intramineral peptides from CB help to unravel the mechanism of calcium salt deposition in nature.

Computational Design and Manufacturing of Sustainable Materials through First-Principles and Materiomics

Engineered materials are ubiquitous throughout society and are critical to the development of modern technology, yet many current material systems are inexorably tied to widespread deterioration of ecological processes. Next-generation material systems can address goals of environmental sustainability by providing alternatives to fossil fuel-based materials and by reducing destructive extraction processes, energy costs, and accumulation of solid waste. However, development of sustainable materials faces several key challenges including investigation, processing, and architecting of new feedstocks that are often relatively mechanically weak, complex, and difficult to characterize or standardize. In this review paper, we outline a framework for examining sustainability in material systems and discuss how recent developments in modeling, machine learning, and other computational tools can aid the discovery of novel sustainable materials. We consider these through the lens of materiomics, an approach that considers material systems holistically by incorporating perspectives of all relevant scales, beginning with first-principles approaches and extending through the macroscale to consider sustainable material design from the bottom-up. We follow with an examination of how computational methods are currently applied to select examples of sustainable material development, with particular emphasis on bioinspired and biobased materials, and conclude with perspectives on opportunities and open challenges.

Bioinformatics and computational analyses of kidney stone modulatory proteins lead to solid experimental evidence and therapeutic potential

In recent biomedical research, bioinformatics and computational analyses have played essential roles for examining experimental findings and database information. Several bioinformatic tools have been developed and made publicly available for analyzing protein sequence, structure, functional motif/domain, and interactions network. Such properties are very helpful to define biochemical and functional roles of the protein(s) of interest. During the past few decades, bioinformatics and computational biotechnology have been widely applied to kidney stone research. This review summarizes commonly used tools and evidence of bioinformatics and computational biotechnology applied to kidney stone disease (KSD) with special emphasis on analyses of the stone modulatory proteins that play critical roles in kidney stone formation. Such analyses lead to solid experimental evidence to demonstrate mechanisms underlying their stone modulatory activities. The findings obtained from such analyses may also lead to better understanding of KSD pathogenesis and to further development of new therapeutic and preventive strategies.

Bacteria-Inspired Aqueous-in-Aqueous Compartmentalization by In Situ Interfacial Biomineralization

Compartmentalization is essential for living cells to orchestrate their biological processes with controlled external influences. Thus, compartmentalization has been a constant theme for cell-mimicking materials. Despite recent advances in engineering compartmentalized materials as synthetic cells and organelles, it remains difficult to produce robust and well-ordered compartments with secluded environments in aqueous surroundings. Nature creates hierarchically ordered compartmentalized materials by utilizing bio-catalyzed mineralization, inspired by which, mechanically robust all-aqueous compartments are developed by engineering a mild biomimetic mineralization at aqueous/aqueous interfaces. The enzyme-induced biomineralization generates a layer of densely-packed particles, acting as an armor to enclose aqueous interiors. This strategy of in situ bio-synthesized compartments is different from current strategies, where compartments are constructed by randomly adsorbed particles at interface, leading to inadequately controlled properties of compartments. To demonstrate the robustness and adaptiveness of the in situ bio-synthesized all-aqueous compartments, these are utilized as drug delivery materials by sequestering protein drugs at their aqueous interiors and releasing when exposing to gastric environments. The study provides new ways to fabricate compartmentalized materials with well-defined properties, unlocking routes to the next generation of self-assembled materials and structures by integrating aqueous two-phase systems with biomineralization.

Recalibrating the calcium trap in amino acid carboxyl groups via classical molecular dynamics simulations

In order to use classical molecular dynamics to complement experiments accurately, it is important to use robust descriptions of the system. The interactions between biomolecules, like aspartic and glutamic acid, and dissolved ions are often studied using standard biomolecular force-fields, where the interactions between biomolecules and cations are often not parameterized explicitly. In this study, we have employed metadynamics simulations to investigate different interactions of Ca with aspartic and glutamic acid and constructed the free energy profiles of Ca²⁺-carboxylate association. Starting from a generally accepted, AMBER-based force field, the association was substantially over and under-estimated, depending on the choice of water model (TIP3P and SPC/fw, respectively). To rectify this discrepancy, we have replaced the default calcium parameters. Additionally, we modified the σ_ij value in the hetero-atomic Lennard-Jones interaction by 0.5% to further improve the interaction between Ca and carboxylate, based on comparison with the experimentally determined association constant for Ca with the carboxylate group of L-aspartic acid. The corrected description retrieved the structural properties of the ion pair in agreement with the original biomolecule - Ca²⁺ interaction in AMBER, whilst also producing an association constant comparable to experimental observations. This refined force field was then used to investigate the interactions between amino acids, calcium and carbonate ions during biogenic and biomimetic calcium carbonate mineralisation.

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.

Transthyretin: From Structural Stability to Osteoarticular and Cardiovascular Diseases

Transthyretin (TTR) is a tetrameric protein transporting hormones in the plasma and brain, which has many other activities that have not been fully acknowledged. TTR is a positive indicator of nutrition status and is negatively correlated with inflammation. TTR is a neuroprotective and oxidative-stress-suppressing factor. The TTR structure is destabilized by mutations, oxidative modifications, aging, proteolysis, and metal cations, including Ca2+. Destabilized TTR molecules form amyloid deposits, resulting in senile and familial amyloidopathies. This review links structural stability of TTR with the environmental factors, particularly oxidative stress and Ca2+, and the processes involved in the pathogenesis of TTR-related diseases. The roles of TTR in biomineralization, calcification, and osteoarticular and cardiovascular diseases are broadly discussed. The association of TTR-related diseases and vascular and ligament tissue calcification with TTR levels and TTR structure is presented. It is indicated that unaggregated TTR and TTR amyloid are bound by vicious cycles, and that TTR may have an as yet undetermined role(s) at the crossroads of calcification, blood coagulation, and immune response.

Escherichia coli templated iron oxide biomineralization under oscillation

Motility is significant in organisms. Studying the influence of motility on biological processes provides a new angle in understanding the essence of life. Biomineralization is a representative process for organisms in forming functional materials. In the present study, we investigated the biomineralization of iron oxides templated by Escherichia coli (E. coli) cells under oscillation. The formation of iron oxide minerals with acicular and banded morphology was observed. The surface charge of E. coli cells contributed to the biomineralization process. The surface components of E. coli cells including lipids, carbohydrates and proteins also have roles in regulating the formation and morphology of iron oxide minerals. As-prepared mineralized iron oxide nanomaterials showed activity in photocatalytic degradation of methylene blue as well as in electrocatalytic hydrogen evolution reaction. This study is helpful not only in understanding motility in biological processes, but also in developing techniques for fabricating functional nanomaterials.

Bio-mineralisation, characterization, and stability of calcium carbonate containing organic matter

The composition of organic matter in biogenic calcium carbonate has long been a mystery, and its role has not received sufficient attention. This study is aimed at elucidating the bio-mineralisation and stability of amorphous calcium carbonate (ACC) and vaterite containing organic matter, as induced by Bacillus subtilis. The results showed that the bacteria could induce various structural forms of CaCO3, such as biogenic ACC (BACC) or biogenic vaterite (BV), using the bacterial cells as their template, and the carbonic anhydrase secreted by the bacteria plays an important role in the mineralisation of CaCO3. The effects of Ca2+ concentration on the crystal structure of CaCO3 were ascertained; when the amount of CaCl2 increased from 0.1% (m/v) to 0.8% (m/v), the ACC was transformed to polycrystalline vaterite. The XRD results demonstrated that the ACC and vaterite have good stability in air or deionised water for one year, or even when heated to 200 °C or 300 °C for 2 h. Moreover, the FTIR results indicated that the BACC or BV is rich in organic matter, and the contents of organic matter in biogenic ACC and vaterite are 39.67 wt% and 28.47 wt%, respectively. The results of bio-mimetic mineralisation experiments suggest that the protein secreted by bacterial metabolism may be inclined to inhibit the formation of calcite, while polysaccharide may be inclined to promote the formation of vaterite. Our findings advance our knowledge of the CaCO3 family and are valuable for future research into organic-CaCO3 complexes.