Calcium-Induced Molecular Rearrangement of Peptide Folds Enables Biomineralization of Vaterite Calcium Carbonate

Biomimetic mineralization of calcium carbonate: modulation of crystal morphology by sticky rice amylopectin in the Ca2+-HCO3- system

Biomineralization is a prevalent and fundamental phenomenon observed in nature. During mineralization, the remarkable specificity and dynamic modulatory capabilities of organic molecules enable the precise control over both the type and structure of minerals at the microscopic level. Drawing inspiration from biomineralization and naturally high concentration of bicarbonate ions in ecosystem waters, this study investigates the biomimetic mineralization process of calcium carbonate within the CaCl2-sticky rice (SR)-NaHCO3 system. Specifically, it examines the effects of SR concentration and calcium ions concentration on the morphology and structure of calcium carbonate crystals. The findings reveal that SR amylopectin, as an organic polysaccharide, effectively influences both the morphology and particle size of calcium carbonate crystals during their crystallization process. The most pronounced modulatory effect is observed at a SR concentration of 0.5 wt%, with a Ca2+: HCO3- molar concentration ratio of 1:4. By providing nucleating coordination sites for calcium carbonate, SR amylopectin facilitates the binding of calcium ions with carbonate ions, thereby promoting the formation of calcium carbonate with an ordered and mineralized structure. The concentration of SR determines the degree of tightness in the branched chain connections within the SR amylopectin structure. When the structural connections are moderately tight and the calcium ions concentration is low, multiple hydroxyl groups within the amylopectin structure coordinate with the same calcium ion. This coordination promotes the uniform growth of calcium carbonate in all directions during the nucleation process, ultimately resulting in the formation of spherical calcium carbonate particles. However, under conditions of high calcium ion concentration, the number of coordination sites becomes insufficient, and the phenomenon of calcium ions being adsorbed by multiple hydroxyl groups within the branched chains weakens. This ultimately results in the formation of cubic-shaped, monocrystalline calcium carbonate particles. The findings can provide a theoretical basis for the practical engineering applications of biomimetic mineralization technologies in bicarbonate-rich environments.

Annexin-derived self-assembling peptide nanostructures for alleviation of calcium oxalate -induced renal injury

The formation of polycrystalline aggregates in the glomerulus or other components of the urinary system is indisputably the most critical step in the formation of kidney stones and calcium oxalate monohydrate (CaC2O4·H2O) is the most prevalent form. On the other hand, Annexin A1 (ANXA1), a calcium-binding protein, markedly increased on the apical surface of renal cells in CaC2O4-induced nephrolithiasis. In this regard, we identified the peptide motif responsible for calcium binding and redesigned it into a self-assembling peptide sequence without disturbing its binding selectivity for the CaC2O4 interface. We developed a salt-dependent strategy to produce self-assembling spherical peptide nanoparticles by using aqueous solutions of R8 peptide and 16-amino acid designed peptide of net charge of -3 (WAEEFLKWLAFIEEFF). Peptide nanoparticles restored cell viability and reduced oxidative stress in MDCK cells triggered by CaC2O4 crystals (80 µg cm- 2) via Nrf2-HO-1 pathway activation. Peptide nanoparticles led to significant protection in urinary biochemistry and reducing calcifications without any toxicity.

Water-Vapor Responsive Metallo-Peptide Nanofibers

Short peptides are versatile molecules for the construction of supramolecular materials. Most reported peptide materials are hydrophobic, stiff, and show limited response to environmental conditions in the solid-state. Herein, we describe a design strategy for minimalistic supramolecular metallo-peptide nanofibers that, depending on their sequence, change stiffness, or reversibly assemble in the solid-state, in response to changes in relative humidity (RH). We tested a series of histidine (H) containing dipeptides with varying hydrophobicity, XH, where X is G, A, L, Y (glycine, alanine, leucine, and tyrosine). The one-dimensional fiber formation is supported by metal coordination and dynamic H-bonds. Solvent conditions were identified where GH/Zn and AH/Zn formed gels that upon air-drying gave rise to nanofibers. Upon exposure of the nanofiber networks to increasing RH, a reduction in stiffness was observed with GH/Zn fibers reversibly (dis-)assembled at 60-70 % RH driven by a rebalancing of hydrogen bonding interactions between peptides and water. When these metallo-peptide nanofibers were deposited on the surface of polyimide films and exposed to varying RH, peptide/water-vapor interactions in the solid-state mechanically transferred to the polymer film, leading to the rapid and reversible folding-unfolding of the films, thus demonstrating RH-responsive actuation.

Structural adaptability and surface activity of peptides derived from tardigrade proteins

Tardigrades are unique micro-organisms with a high tolerance to desiccation. The protection of their cells against desiccation involves tardigrade-specific proteins, which include the so-called cytoplasmic abundant heat soluble (CAHS) proteins. As a first step towards the design of peptides capable of mimicking the cytoprotective properties of CAHS proteins, we have synthesized several model peptides with sequences selected from conserved CAHS motifs and investigated to what extent they exhibit the desiccation-induced structural changes of the full-length proteins. Using circular dichroism spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations, we have found that the CAHS model peptides are mostly disordered, but adopt a moreα $$ \alpha $$ -helical structure upon addition of 2,2,2-trifluoroethanol, which mimics desiccation. This structural behavior is similar to that of full-length CAHS proteins, which also adopt more ordered conformations upon desiccation. We also have investigated the surface activity of the peptides at the air/water interface, which also mimics partial desiccation. Interestingly, sum-frequency generation spectroscopy shows that all model peptides are surface active and adopt a helical structure at the air/water interface. Our results suggest that amino acids with high helix-forming propensities might contribute to the propensity of these peptides to adopt a helical structure when fully or partially dehydrated. Thus, the selected sequences retain part of the CAHS structural behavior upon desiccation, and might be used as a basis for the design of new synthetic peptide-based cryoprotective materials.

An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation

Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.

Role of Water during the Early Stages of Iron Oxyhydroxide Formation by a Bacterial Iron Nucleator

Understanding the nucleation of iron oxides and the underlying hydrolysis of aqueous iron species is still challenging, and molecular-level insights into the orchestrated response of water, especially at the hydrolysis interface, are lacking. We follow iron(III) hydrolysis in the presence of a synthetic bacterial iron nucleator, which is a magnetosome membrane specific peptide, by using a constant pH titration technique. Three distinct hydrolysis regimes were identified. Interface-selective sum frequency generation (SFG) spectroscopy was used to probe the interfacial reaction and water in direct contact with the peptide. SFG data reveal that iron(III) species react quickly with interfacial peptides while continuously enhancing water alignment into the later stages of hydrolysis. The gradually aligning water molecules are associated with initially promoted (regimes I and II) and later suppressed (regime III) hydrolysis after the saturation of water alignment has occurred until regime II. These interfacial insights are crucial for understanding the early stage of iron oxide biomineralization.

Mussel-Inspired Polydopamine Composite Mesoporous Bioactive Glass Nanoparticles: An Exploration of Potential Metal-Ion Loading Platform and In Vitro Bioactivity

Exploring new approaches to realize the possibility of incorporating biologically active elements into mesoporous silicate bioactive glass nanoparticles (MBG NPs) and guaranteeing their meso- structural integrity and dimensional stability has become an attractive and interesting challenge in biomaterials science. We present a postgrafting strategy for introducing different metal elements into MBG NPs. This strategy is mediated by polydopamine (PDA) coating, achieving uniform loading of copper or copper-cobalt on the particles efficiently and ensuring the stability of MBG NPs in terms of particle size, mesoporous structure, and chemical structure. However, the PDA coating reduced the ion-binding free energy of the MBG NPs for calcium and phosphate ions, resulting in the deposition of minimal CaP clusters on the PDA@MBG NP surface when immersed for 7 days in simulated body fluid, indicating the absence of hydroxyapatite mineralization.

Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals

Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.

Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide

Two-dimensional (2D) materials have attracted attention for potential applications in light harvesting, catalysis, and molecular electronics. Mineral proteins involved in hard tissue biogenesis can produce 2D structures with high fidelity by using sustainable production routes. This study shows that a peptide mimic based on the catalytic triad of the marine sponge protein silicatein catalyzes the formation of nanometer thin and stable sheets of silicon dioxide and titanium dioxide.

Cooperative Metal Ion Coordination to the Short Self-Assembling Peptide Promotes Hydrogelation and Cellular Proliferation

Non-covalent interactions among short peptides and proteins led to their molecular self-assembly into supramolecular packaging, which provides the fundamental basis of life. These biomolecular assemblies are highly susceptible to the environmental conditions, including temperature, light, pH, and ionic concentration, thus inspiring the fabrication of a new class of stimuli-responsive biomaterials. Here, we report for the first time the cooperative effect of the divalent metal ions to promote hydrogelation in the short collagen inspired self-assembling peptide for developing advanced biomaterials. Introduction of the biologically relevant metal ions (Ca²⁺ /Mg²⁺ ) to the peptide surpasses its limitation to self-assemble into a multi-scale structure at physiological pH. In particular, in presence of metal ions, the negatively charged peptide showed a distinct shift in its equilibrium point of gelation and demonstrated conversion from sol to gel and thus enabling the scope of fabricating an advanced biomaterial for controlling cellular behaviour. Interestingly, tunable mechanical strength and improved cellular response were observed within ion-coordinated peptide hydrogels compared to the peptide gelator. Microscopic analyses, rheological assessment, and biological studies established the importance of utilizing a novel strategy by simply using metal ions to modulate the physical and biological attributes of CIPs to construct next-generation biomaterials. This article is protected by copyright. All rights reserved.

Simulating the binding of key organic functional groups to aqueous calcium carbonate species

The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.

Membrane Structure of Aquaporin Observed with Combined Experimental and Theoretical Sum Frequency Generation Spectroscopy

High-resolution structural information on membrane proteins is essential for understanding cell biology and for the structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide angstrom-level information about the structure of membrane proteins, yet for XRD experiments, proteins are removed from their native membrane environment, chemically stabilized, and crystallized, all of which can compromise the conformation. Here, we describe how a combination of surface-sensitive vibrational spectroscopy and molecular dynamics simulations can account for the native membrane environment. We observe the structure of a glycerol facilitator channel (GlpF), an aquaporin membrane channel finely tuned to selectively transport water and glycerol molecules across the membrane barrier. We find subtle but significant differences between the XRD structure and the inferred in situ structure of GlpF.

Interaction of Amyloid-β-(1-42) Peptide and Its Aggregates with Lipid/Water Interfaces Probed by Vibrational Sum-Frequency Generation Spectroscopy

In this study, we use surface-sensitive vibrational sum-frequency generation (VSFG) spectroscopy to investigate the interaction between model lipid monolayers and Aβ(1-42) in its monomeric and aggregated states. Combining VSFG with atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence measurements, we found that only small aggregates with probably a β-hairpin-like structure adsorbed to the zwitterionic lipid monolayer (DOPC). In contrast, larger aggregates with an extended β-sheet structure adsorbed to a negatively charged lipid monolayer (DOPG). The adsorption of small, initially formed aggregates strongly destabilized both monolayers, but only the DOPC monolayer was completely disrupted. We showed that the intensity of the amide-II' band in achiral (SSP) and chiral (SPP) polarization combinations increased in time when Aβ(1-42) aggregates accumulated at the DOPG monolayer. Nevertheless, almost no adsorption of preformed mature fibrils to DOPG monolayers was detected. By performing spectral VSFG calculations, we revealed a clear correlation between the amide-II' signal and the degree of amyloid aggregates (e.g., oligomers or (proto)fibrils) of various Aβ(1-42) structures. The calculations showed that only structures with a significant amyloid β-sheet content have a strong amide-II' intensity, in line with previous Raman studies. The combination of the presented results substantiates the amide-II(') band as a legitimate amyloid marker.

Backbone Structure of Diatom Silaffin Peptide R5 in Biosilica Determined by Combining Solid-State NMR with Theoretical Sum-Frequency Generation Spectra

Silaffin peptide R5 is key for the biogenesis of silica cell walls of diatoms. Biosilification by the R5 peptide has potential in biotechnology, drug development, and materials science due to its ability to precipitate stable, high fidelity silica sheets and particles. A true barrier for the design of novel peptide-based architectures for wider applications has been the limited understanding of the interfacial structure of R5 when precipitating silica nanoparticles. While R5-silica interactions have been studied in detail at flat surfaces, the structure within nanophase particles is still being debated. We herein elucidate the conformation of R5 in its active form within silica particles by combining interface-specific vibrational spectroscopy data with solid-state NMR torsion angles using theoretical spectra. Our calculations show that R5 is structured and undergoes a conformational transition from a strand-type motif in solution to a more curved, contracted structure when interacting with silica precursors.

Assembly of iron oxide nanosheets at the air-water interface by leucine-histidine peptides

The fabrication of inorganic nanomaterials is important for a wide range of disciplines. While many purely inorganic synthetic routes have enabled a manifold of nanostructures under well-controlled conditions, organisms have the ability to synthesize structures under ambient conditions. For example, magnetotactic bacteria, can synthesize tiny 'compass needles' of magnetite (Fe3O4). Here, we demonstrate the bio-inspired synthesis of extended, self-supporting, nanometer-thin sheets of iron oxide at the water-air interface through self-assembly using small histidine-rich peptides.

Intrinsically Disordered Osteopontin Fragment Orders During Interfacial Calcium Oxalate Mineralization

Calcium oxalate (CaC2 O4 ) is the major component of kidney stone. The acidic osteopontin (OPN) protein in human urine can effectively inhibit the growth of CaC2 O4 crystals, thereby acting as a potent stone preventer. Previous studies in bulk solution all attest to the importance of binding and recognition of OPN at the CaC2 O4 mineral surface, yet molecular level insights into the active interface during CaC2 O4 mineralization are still lacking. Here, we probe the structure of the central OPN fragment and its interaction with Ca2+ and CaC2 O4 at the water-air interface using surface-specific non-linear vibrational spectroscopy. While OPN peptides remain largely disordered in solution, our results reveal that the bidentate binding of Ca2+ ions refold the interfacial peptides into well-ordered and assembled β-turn motifs. One critical intermediate directs mineralization by releasing structural freedom of backbone and binding side chains. These insights into the mineral interface are crucial for understanding the pathological development of kidney stones and possibly relevant for calcium oxalate biomineralization in general.

Developments and Ongoing Challenges for Analysis of Surface-Bound Proteins

Proteins at surfaces and interfaces play important roles in the function and performance of materials in applications ranging from diagnostic assays to biomedical devices. To improve the performance of these materials, detailed molecular structure (conformation and orientation) along with the identity and concentrations of the surface-bound proteins on those materials must be determined. This article describes radiolabeling, surface plasmon resonance, quartz crystal microbalance with dissipation, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, sum frequency generation spectroscopy, and computational techniques along with the information each technique provides for characterizing protein films. A multitechnique approach using both experimental and computation methods is required for these investigations. Although it is now possible to gain much insight into the structure of surface-bound proteins, it is still not possible to obtain the same level of structural detail about proteins on surfaces as can be obtained about proteins in crystals and solutions, especially for large, complex proteins. However, recent results have shown it is possible to obtain detailed structural information (e.g., backbone and side chain orientation) about small peptides (5-20 amino sequences) on surfaces. Current studies are extending these investigations to small proteins such as protein G B1 (∼6 kDa). Approaches for furthering the capabilities for characterizing the molecular structure of surface-bound proteins are proposed.

Monitoring Crystallization Processes in Confined Porous Materials by Dynamic Nuclear Polarization Solid-State Nuclear Magnetic Resonance

Establishing mechanistic understanding of crystallization processes at the molecular level is challenging, as it requires both the detection of transient solid phases and monitoring the evolution of both liquid and solid phases as a function of time. Here, we demonstrate the application of dynamic nuclear polarization (DNP) enhanced NMR spectroscopy to study crystallization under nanoscopic confinement, revealing a viable approach to interrogate different stages of crystallization processes. We focus on crystallization of glycine within the nanometric pores (7-8 nm) of a tailored mesoporous SBA-15 silica material with wall-embedded TEMPO radicals. The results show that the early stages of crystallization, characterized by the transition from the solution phase to the first crystalline phase, are straightforwardly observed using this experimental strategy. Importantly, the NMR sensitivity enhancement provided by DNP allows the detection of intermediate phases that would not be observable using standard solid-state NMR experiments. Our results also show that the metastable β polymorph of glycine, which has only transient existence under bulk crystallization conditions, remains trapped within the pores of the mesoporous SBA-15 silica material for more than 200 days.

Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water

Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a β-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation.

Ice-nucleating proteins promote ice formation at high sub-zero temperatures, but the mechanism is still unclear. The authors investigate a model ice-nucleating protein at the air-water interface using vibrational sum frequency generation spectroscopy and simulations, revealing its reorientation at low temperatures, which increases contact with water molecules and promotes their ordering.

Direct Evidence That Mutations within Dysferlin's C2A Domain Inhibit Lipid Clustering

Mechanical stress on sarcolemma can create small tears in the muscle cell membrane. Within the sarcolemma resides the multidomain dysferlin protein. Mutations in this protein render it unable to repair the sarcolemma and have been linked to muscular dystrophy. A key step in dysferlin-regulated repair is the binding of the C2A domain to the lipid membrane upon increased intracellular calcium. Mutations mapped to this domain cause loss of binding ability of the C2A domain. There is a crucial need to understand the geometry of dysferlin C2A at a membrane interface as well as cell membrane lipid reorientation when compared to that of a mutant. Here, we describe a comparison between the wild-type dysferlin C2A and a mutation to the conserved aspartic acids in the domain binding loops. To identify both the geometry and the cell membrane lipid reorientation, we applied sum frequency generation (SFG) vibrational spectroscopy and coupled it with simulated SFG spectra to observe and quantify the interaction with a model cell membrane composed of phosphotidylserine and phosphotidylcholine. Observed changes in surface pressure demonstrate that calcium-bridged electrostatic interactions govern the initial interaction of the C2A domains docking with a lipid membrane. SFG spectra taken from the amide-I region for the wild type and variant contain features near 1642, 1663, and 1675 cm^-1 related to the C2A domain β-sandwich secondary structure, indicating that the domain binds in a specific orientation. Mapping simulated SFG spectra to the experimentally collected spectra indicated that both wild-type and variant domains have nearly the same orientation to the membrane surface. However, examining the ordering of the lipids that make up a model membrane using SFG, we find that the wild type clusters the lipids as seen by the increase in the ratio of the CD₃ and CD₂ symmetric intensities by 170% for the wild type and by 120% for the variant. This study highlights the capabilities of SFG to probe with great detail biological mutations in proteins at cell membrane interfaces.

Biomineralization at fluid interfaces

Biomineralization is of paramount importance for life on Earth. The delicate balance of physicochemical interactions at the interface between organic and inorganic matter during all stages of biomineralization resembles an extremely high complexity. The coordination of this sophisticated biological machinery and physicochemical scenarios is certainly a wonderful show of nature. Understanding of the biomineralization processes is still far from complete. The recent advances in biomineralization research from the Colloid and Interface Science perspective are reviewed herein. The synergy between this two fields of research is demonstrated. The unique opportunities offered by purposefully designed fluid interfaces, mainly Langmuir monolayers are presented. Biomedical applications of biomineral-based nanostructures are discussed, showing their improved biocompatibility and on-demand delivery features. A brief guide to the array of state-of-the-art experimental techniques for unraveling the mechanisms of biomineralization using fluid interfaces is included. In summary, the fruitful and exciting crossroad between Colloid and Interface Science with Biomineralization is exhibited.

Cell-tailored calcium carbonate particles with different crystal forms from nanoparticle to nano/microsphere

Inspired by biomineralization, the first synthesis of size-tunable calcium carbonates from nanoparticles (YC-CaCO3 NPs) to nano/microspheres (YC-CaCO3 N/MSs) with a porous structure was accomplished using a facile method under the mediation of the secretion from yeast cells (YCs). The biomolecules derived from the secretion of YCs were used as conditioning and stabilizing agents to control the biosynthesis of the YC-CaCO3 materials. The morphology and crystal forms of YC-CaCO3 materials can be affected by the biomolecules from the secretion of YCs. With increasing concentrations of biomolecules, the morphologies of the obtained CaCO3 materials changed from nanoparticles to nano/microspheres with a porous structure, while the crystal forms transformed from amorphous to calcite. Functional investigations showed that YC-CaCO3 NSs with a porous structure effectively acted as anticancer drug carriers with accurate and selective drug release in tumor tissue, which suggests that they have great potential to function as a therapeutic delivery system. These application features are mainly attributed to the satisfactory biocompatibility and biodegradability, high drug-loading capacity, and pH-dependent sustained drug release performance of the porous YC-CaCO3 NSs. The biomimetic synthesis strategy of YC-CaCO3 materials mediated by YC secretion not only helps to shed light on the biomineralization mechanism in organisms, but may also lead to a new means of biosynthesizing organic-inorganic nanocomposites.

Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Understanding the assembly of proteins at the air-water interface (AWI) informs the formation of protein films, emulsion properties, and protein aggregation. Determination of protein conformation and orientation at an interface is difficult to resolve with a single experimental or simulation technique alone. To date, the interfacial structure of even one of the most widely studied proteins, lysozyme, at the AWI remains unresolved. In this study, molecular dynamics (MD) simulations are used to determine if the protein adopts a side-on, head-on, or axial orientation at the AWI with two different forcefields, GROMOS-53a6 + SPC/E and a99SB-disp + TIP4P-D. Vibrational sum frequency generation (SFG) spectroscopy experiments and spectral SFG calculations validate consistency between the structure determined from MD and experiments. Overall, we show with strong agreement that lysozyme adopts an axial conformation at pH 7. Further, we provide molecular-level insight as to how pH influences the binding domains of lysozyme resulting in side-on adsorption near the isoelectric point of the lysozyme.

The Crystallization Process of Vaterite Microdisc Mesocrystals via Proto-Vaterite Amorphous Calcium Carbonate Characterized by Cryo-X-ray Absorption Spectroscopy

Investigation on the formation mechanism of crystals via amorphous precursors has attracted a lot of interests in the last years. The formation mechanism of thermodynamically meta-stable vaterite in pure alcohols in the absence of any additive is less known. Herein, the crystallization process of vaterite microdisc mesocrystals via proto-vaterite amorphous calcium carbonate (ACC) in isopropanol was tracked by using Ca K-edge X-ray absorption spectroscopy (XAS) characterization under cryo-condition. Ca K-edge X-ray absorption near edge structure (XANES) spectra show that the absorption edges of the Ca ions of the vaterite samples with different crystallization times shift to lower photoelectron energy while increasing the crystallization times from 0.5 to 20 d, indicating the increase of crystallinity degree of calcium carbonate. Ca K-edge extended X-ray absorption fine structure (EXAFS) spectra exhibit that the coordination number of the nearest neighbor atom O around Ca increases slowly with the increase of crystallization time and tends to be stable as 4.3 (±1.4). Crystallization time dependent XANES and EXAFS analyses indicate that short-range ordered structure in proto-vaterite ACC gradually transform to long-range ordered structure in vaterite microdisc mesocrystals via a non-classical crystallization mechanism.

Illustrating Interfacial Interaction between Honey Bee Venom Phospholipase A2 and Supported Negatively Charged Lipids with Sum Frequency Generation and Laser Scanning Confocal Microscopy

Phospholipase A₂ is an important enzyme species which can widely be found in animals, plants, bacteria, and so on. A large number of studies have shown that phospholipase A₂ is highly catalytic toward the lipids. Here, sum frequency generation (SFG) vibrational spectroscopy and laser scanning confocal microscopy (LSCM) were applied to study the interaction between honey bee venom phospholipase A₂ (bvPLA₂) and the negatively charged DPPG bilayer. In both cases without and with the calcium ions (Ca²⁺), the bvPLA₂ molecules were adsorbed onto the outer leaflet surface with the orientational order, and the adsorbed bvPLA₂ molecules damaged the order of the packed outer leaflet. In comparison to the case without Ca²⁺, the addition of Ca²⁺ can accelerate the attaching process of bvPLA₂ to the outer leaflet surface and decelerate the process of damaging the outer leaflet order. The experimental result also confirmed, with the help of the Ca²⁺, the DPPG molecules in the outer leaflet were hydrolyzed, with both hydrolysates, that is, lysophospholipids and fatty acids, remaining at the interface, showing a distinct difference from previous published literatures regarding neutral lipids [Phys. Chem. Chem. Phys. 2018, 20, 63-67] and PLA₁ [Langmuir 2019, 35, 12831-12838].

Acidic Environment Significantly Alters Aggregation Pathway of Human Islet Amyloid Polypeptide at Negative Lipid Membrane

The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) at cell membrane has a close relationship with the development of type 2 diabetes (T2DM). This aggregation process is susceptible to various physiologically related factors, and systematic studies on condition-mediated hIAPP aggregation are therefore essential for a thorough understanding of the pathology of T2DM. In this study, we combined surface-sensitive amide I and amide II spectral signals from the protein backbone, generated simultaneously in a highly sensitive femtosecond broad-band sum frequency generation vibrational spectroscopy system, to examine the effect of environmental pH on the dynamical structural changes of hIAPP at membrane surface in situ and in real time. Such a combination can directly discriminate the formation of β-hairpin-like monomer and oligomer/fibril at the membrane surface. It is evident that, in an acidic milieu, hIAPP slows down its conformational evolution and alters its aggregation pathway, leading to the formation of off-pathway oligomers. When matured hIAPP aggregates are exposed to basic subphase, partial conversion from β-sheet oligomers into ordered β-sheet fibrillar structures is observed. When exposed to acidic environment, however, hIAPP fibrils partially converse into more loosely patterned β-sheet oligomeric structures.

Phase selection of calcium carbonate crystals under the induction of lignin monomer model compounds

The formation and application of ‘cinnamic acid & CaCO₃ crystals’ (CACs) induced by a lignin monomer compound.

Otoferlin C2F Domain-Induced Changes in Membrane Structure Observed by Sum Frequency Generation

Proteins that contain C2 domains are involved in a variety of biological processes, including encoding of sound, cell signaling, and cell membrane repair. Of particular importance is the interface activity of the C-terminal C2F domain of otoferlin due to the pathological mutations known to significantly disrupt the protein's lipid membrane interface binding activity, resulting in hearing loss. Therefore, there is a critical need to define the geometry and positions of functionally important sites and structures at the otoferlin-lipid membrane interface. Here, we describe the first in situ probe of the protein orientation of otoferlin's C2F domain interacting with a cell membrane surface. To identify this protein's orientation at the lipid interface, we applied sum frequency generation (SFG) vibrational spectroscopy and coupled it with simulated SFG spectra to observe and quantify the otoferlin C2F domain interacting with model lipid membranes. A model cell membrane was built with equal amounts of phosphatidylserine and phosphatidylcholine. SFG measurements of the lipids that make up the model membrane indicate a 62% increase in amplitude from the SFG signal near 2075 cm^-1 upon protein interaction, suggesting domain-induced changes in the orientation of the lipids and possible membrane curvature. This increase is related to lipid ordering caused by the docking interaction of the otoferlin C2F domain. SFG spectra taken from the amide-I region contain features near 1630 and 1670 cm^-1 related to the C2F domains beta-sandwich secondary structure, thus indicating that the domain binds in a specific orientation. By mapping the simulated SFG spectra to the experimentally collected SFG spectra, we found the C2F domain of otoferlin orients 22° normal to the lipid surface. This information allows us to map what portion of the domain directly interacts with the lipid membrane.

Peptide-Controlled Assembly of Macroscopic Calcium Oxalate Nanosheets

The fabrication of two-dimensional (2D) biomineral nanosheets is of high interest owing to their promise for applications in electronics, filtration, catalysis, and chemical sensing. Using a facile approach inspired by biomineralization in nature, we fabricate laterally macroscopic calcium oxalate nanosheets using β-folded peptides. The template peptides are composed of repetitive glutamic acid and leucine amino acids, self-organized at the air-water interface. Surface-specific sum frequency generation spectroscopy and molecular dynamics simulations reveal that the formation of oxalate nanosheets relies on the peptide-Ca²⁺ ion interaction at the interface, which not only restructures the peptides but also templates Ca²⁺ ions into a calcium oxalate dihydrate lattice. Combined, this enables the formation of a critical structural intermediate in the assembly pathway toward the oxalate sheet formation. These insights into peptide-ion interfacial interaction are important for designing novel inorganic 2D materials.

Structure of von Willebrand factor A1 on polystyrene determined from experimental and calculated sum frequency generation spectra

The blood-clotting protein von Willebrand factor (vWF) can be activated by small molecules, high shear stress, and interactions with interfaces. It subsequently binds platelet receptor glycoprotein Ibα (GPIbα) at the surface of platelets, thereby playing a crucial role in blood clotting due to platelet activation, which is an important process to consider in the design of cardiovascular implants and biomaterials used in blood-contacting applications. The influence of surfaces on the activation and the molecular-level structure of surface-bound vWF is largely unknown. Recent studies have indicated that when bound to hydrophobic polystyrene (PS), the A1 domain of vWF remains accessible for GPIbα binding. However, the detailed secondary structure and exact orientation of vWF A1 at the PS surface is still unresolved. Here, the authors resolve these features by studying the system with sum-frequency generation (SFG) spectroscopy. The data are consistent with a scenario where vWF A1 maintains a native secondary structure when bound to PS. Comparison of experimental and calculated SFG spectra combined with previously reported time-of-flight secondary ion mass spectrometry data suggests that A1 assumes an orientation with the GPIbα binding domain oriented away from the solid surface and exposed to the solution phase. This structural information will benefit future in vitro experiments with surface-adsorbed A1 domain and may have relevance for the design of novel blood-contacting biomaterials and wound-healing applications.

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces

Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or complement to experimental structure determination is molecular simulation. Rosetta is one software suite that models protein-surface interactions, but Rosetta is normally benchmarked on soluble proteins. For surface interactions, the validity of the energy function is uncertain because it is a combination of independent parameters from energy functions developed separately for solution proteins and mineral surfaces. Here, we assess the performance of the RosettaSurface algorithm and test the accuracy of its energy function by modeling the adsorption of leucine/lysine (LK)-repeat peptides on methyl- and carboxy-terminated self-assembled monolayers (SAMs). We investigated how RosettaSurface predictions for this system compare with the experimental results, which showed that on both surfaces, LK-α peptides folded into helices and LK-β peptides held extended structures. Utilizing this model system, we performed a parametric analysis of Rosetta's Talaris energy function and determined that adjusting solvation parameters offered improved predictive accuracy. Simultaneously increasing lysine carbon hydrophilicity and the hydrophobicity of the surface methyl head groups yielded computational predictions most closely matching the experimental results. De novo models still should be interpreted skeptically unless bolstered in an integrative approach with experimental data.

Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water

Combined SFG/MD analysis together with spectral calculations revealed that type III antifreeze proteins adsorbed at the air–water interface maintains a native state and adopts an orientation that leads to a partial decoupling of its ice-binding site from water.