Nacre Proteins Research Articles

Reinforcement learning design framework for nacre-like structures optimized for pre-existing crack resistance

Nacre is known for its uniquely high toughness and lightweight capabilities. Its unique structure is composed of soft nacre proteins and stiff calcium carbonates, allowing it to deflect cracks that expand in straight lines to increase energy dissipation. However, nacre microstructures are challenging to mimic due to the intractable number of combinations in the design space. We thus propose a reinforcement learning (RL) framework to efficiently design a high-toughness nacre-like structure. By designing local structures at the crack tip, we incorporated reinforcement learning with finite element to optimize the structure by replacing the soft and stiff materials in the design space. Starting from the initial unit cell, where the majority of the unit cell consists of soft materials, our method gradually improves the cell by arranging stiff and soft materials on the unit cell to achieve higher toughness. The optimized designs exhibit crack-insensitive behavior and excellent crack resistance when subjected to finite element simulation and experimental testing. This design framework can be used in synthetic instruments that require rapid construction rearrangements such as biomaterials and unexposed substructures, increasing their mechanical performance.

Micropatterning biomineralization with immobilized mother of pearl proteins

In response to the drawbacks of autograft donor-site morbidity and bone morphogenetic protein type 2 (BMP2) carcinogenesis and ectopic bone formation, there has been an increased research focus towards developing alternatives capable of achieving spatial control over bone formation. Here we show for the first time both osteogenic differentiation and mineralization (from solution or mediated by cells) occurring within predetermined microscopic patterns. Our results revealed that both PEGylated BMP2 and nacre proteins induced stem cell osteodifferentiation in microscopic patterns when these proteins were covalently bonded in patterns onto polyethylene glycol diacrylate (PEGDA) hydrogel substrates; however, only nacre proteins induced mineralization localized to the micropatterns. These findings have broad implications on the design and development of orthopedic biomaterials and drug delivery.

Temperature elevation and acidification damage microstructure of abalone via expression change of crystal induction genes

Ocean warming and acidification caused by global climate change interferes with the shell growth of mollusks. In abalone Haliotis discus hannai, the microstructural changes in the shell under stress are unclear, and the effect of thermal stress on biomineralization is unknown. The lack of gene information has also hampered the study of abalone biomineralization mechanisms. In this study, the microstructure of reconstructed shell in H. discus hannai was observed to determine the effects of thermal and acidification stress on shell growth. Three nacre protein genes, Hdh-AP7, Hdh-AP24, and Hdh-perlustrin, were characterized, and their expression pattern during shell repair was measured under thermal and acidification stress and compared with those of two known biomineralization-related genes, Hdh-AP-1 and Hdh-defensin. The stress resulted in aragonite plates with corroded or irregular microstructures. The gene expression of two nacre proteins (Hdh-AP7 and Hdh-AP24), which directly induce crystal formation, were more sensitive to thermal stress than to acidification, but the expression of the regulatory nacre protein (Hdh-perlustrin) and the two known genes (Hdh-AP-1 and Hdh-defensin), which are also related to immunity, showed an interlinked, complex pattern change. We concluded that high temperature and acidification damages the shell microstructure by disturbing the expression pattern of biomineralization-related genes.

A Complicated Relationship: Glycosylation, Ca(II), and Primary Sequence Affect the Interactions and Kinetics between Two Model Mollusk Shell Intracrystalline Nacre Proteins.

The formation of the mollusk shell requires the participation of proteins, many of which may be interactive with one another. We examined a model protein pair system from the mollusk Haliotis rufescens, wherein we probed the interactions between recombinant forms of two major nacre layer proteins, AP7, and the glycoprotein, AP24. Here, the focus was on the impact that the AP24 glycosylation and primary sequence had on AP24-AP7 binding. We find that both the glycosylated and nonglycosylated variants of AP24 bound to AP7 but with different quantities, kinetics, and internal rearrangements. Moreover, the binding of AP7 with nonglycosylated and glycosylated AP24 was found to be Ca(II)-dependent and -independent, respectively. Yet both variants of AP24 combine with AP7 to form hybrid hydrogel particles that are similar in their physical properties. Thus, AP7 and AP24 protein sequences are interactive and form hydrogels, but the interactions are tuned by glycosylation and Ca(II). These features may have an impact on the nacre matrix formation.

Cloning and characterization of a novel Lustrin A gene from Haliotis discus hannai.

Lustrin A is the first nacre protein with specific structure and amino acid residue content that was identified in abalone; since its identification, homologs have been found in several abalone species. In this study, we isolated and cloned the complete cDNA of Lustrin A from Haliotis discus hannai, which was named Hdh-Lustrin A. Hdh-Lustrin A has characteristic cysteine- and proline-rich domains, glycine- and serine-rich domains, and a whey acidic protein (WAP)-like C-terminus. The cysteine- and proline-rich domains showed internal similarity repeats that arrayed in gene coding region, and the phylogenetic tree of these repeats indicated that the similarity of structural repetitive unit components in different abalone species, reflecting their evolutionary distance. A tissue distribution analysis showed that the mRNA level of Hdh-Lustrin A has tissue-specific expression in mantle. Under lipopolysaccharide (LPS) challenge, Hdh-Lustrin A showed a significantly increase, while it showed a more complex pattern with two peaks in the process of shell regeneration. Moreover, acidification and warming raised the expression level of Hdh-Lustrin A in shell regeneration in two different manners; acidification raised the gene expression in quick response, in contrast the long run in warming treatment. Similar pattern also has been detected in immune reaction and the thermal treatments. These results suggest that the Hdh-Lustrin A is a nacre protein, which can be distinguished by its cysteine- and proline-rich domain. It involves in shell regeneration and innate immunity in abalone, and its expression pattern during shell regeneration can be disrupted by physicochemical properties of the environment.

Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii

BackgroundThe pearl oyster Pinctada fucata martensii (Pfu.), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues.ResultsA total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log2 (fold change) | ≥2 and false discovery rate < 0.001). Tyrosine metabolism, calcium signalling pathway, phototransduction, melanogenesis pathways and rhodopsin related Gene Ontology (GO) terms were enriched with significant differentially expressed genes (DEGs) in transcriptomic. Proteomic sequencing identified 1769 proteins, of which 51 were significantly differentially expressed in yellow shell oysters. Calmodulin, N66 matrix protein, nacre protein and Kazal-type serine protease inhibitor were up-regulated in yellow shell oysters at both mRNA and protein levels, while glycine-rich protein shematrin-2, mantle gene 4, and sulphide: quinone oxidoreductase were down-regulated at two omics levels. Particularly, calmodulin, nacre protein N16.3, mantle gene 4, sulphide: quinone oxidoreductase, tyrosinase-like protein 3, cytochrome P450 3A were confirmed by quantitative real-time PCR. Yellow shell oysters possessed higher total carotenoid content (TCC) compared than black shell oyster based on spectrophotography.ConclusionsThe yellow phenotype of pearl oysters, characterised by higher total carotenoids content, may reflect differences in retinal and rhodopsin metabolism, melanogenesis, calcium signalling pathway and biomineralisation. These results provide insights for exploring the relationships between calcium regulation, biomineralisation and yellow shell colour pigmentation.

Transcriptome analysis reveals functional roles of nacreous protein N16 in prednisolone-induced osteoporotic zebrafish

N16 is an active protein isolated and screened from nacre proteins. Our previous studies have shown that N16 exerted a good effect on osteoporosis caused by dexamethasone on female rats. In order to further confirm the action of N16 against glucocorticoid-induced osteoporosis (GIOP) and clarify its possible mechanisms, prednisolone-treated larval zebrafish (Danio rerio) model was adopted. Administration of N16 resulted in a significant increase of vertebral bone density of osteoporotic zebrafish, indicating a good effect of N16 against GIOP. Transcriptomic sequencing analysis was then performed to investigate the mechanisms of the action of N16 against GIOP. It was observed that N16 modulated the osteoporotic phenotype by up-regulating the osteoblastic characteristic genes and down-regulating the osteoclastic characteristic genes in zebrafish.

In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix

BackgroundThe shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date.MethodsThe shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing.ResultsWe identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins.ConclusionsThe H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly.

Noninvasive Microcomputerized X-ray Tomography Visualization of Mineralization Directed by Sea Urchin- and Nacre-Specific Proteins

The biomineralization process offers novel principles for crystal engineering and solid-state chemistry, but to achieve this we must first understand how organisms such as the mollusk and sea urchin craft skeletal elements such as the shell and embryonic spicule, respectively. In vitro studies of mollusk- and sea urchin-associated proteins reveal that these proteins form hydrogel particles that control the nucleation process, assemble mineral nanoparticles, and modify the surfaces and interiors of existing crystals. However, visualization of these processes is hampered by destructive and invasive methods such as those used for conventional scanning electron microscopy/transmission electron microscopy. In this report we detail the novel use of microcomputerized X-ray tomography (μCT) imaging to nondestructively investigate the in vitro calcium carbonate mineralization process in the presence of a recombinant sea urchin spicule matrix protein, rSpSM50, and a recombinant mollusk shell nacre protein, rPif97. Relative to the protein-free control scenario, both proteins generate calcite crystals that are consistent with the results obtained from previous studies, but with μCT we discovered new features; each protein generates a different number of mineral deposits, exhibits unique domains or motifs, and creates a stratification of mineral phases into layers. These results coincide with the known function of these proteins in vitro and in situ, and provide new information regarding biomineralization protein hydrogels and how they influence nucleation and crystal growth. We foresee that μCT imaging could, for appropriately sized systems, offer a bridge between in vitro experiments and in situ investigations of time-resolved nucleation and crystal growth phenomena in organisms, tissues, and synthetic materials.

Intracrystalline incorporation of nacre protein hydrogels modifies the mechanical properties of calcite crystals: a microcompression study.

The fracture toughness of mollusk shell nacre has been attributed to many factors, one of which is the intracrystalline incorporation of nacre-specific proteins. Although mechanical force measurements have been made on the nacre layer and on individual calcium carbonate crystals containing occluded organic molecules and macromolecules, there are few if any studies which examine the impact of occluded proteins on the mechanical properties of calcium carbonate crystals. To remedy this, we performed microcompression studies of calcite crystals grown in the presence and absence of two recombinant nacre proteins, r-AP7 (H. rufescens, intracrystalline proteome) and r-n16.3 (P. fucata, framework proteome), both of which are known aggregators that form hydrogel nanoinclusions within in vitro calcite. We find that, relative to protein-free calcite, the intracrystalline inclusion of either r-AP7 or r-n16.3 nacre protein hydrogels within the calcite crystals leads to a reduction in strength. However, nacre protein-modified crystals were found to exhibit elastic deformation under force compared to control scenarios, with no discernable differences noted between intracrystalline or framework protein-modified crystals. We conclude from our in vitro microcompression studies that the intracrystalline incorporation of nacre proteins can contribute to fracture-resistance of the crystalline phase by significantly reducing both modulus AND critical strength.

A Model Sea Urchin Spicule Matrix Protein, rSpSM50, Is a Hydrogelator That Modifies and Organizes the Mineralization Process.

In the purple sea urchin Strongylocentrotus purpuratus, the formation and mineralization of fracture-resistant skeletal elements such as the embryonic spicule require the combinatorial participation of numerous spicule matrix proteins such as SpSM50. However, because of its limited abundance and solubility issues, it has been difficult to pursue extensive in vitro biochemical studies of SpSM50 protein and deduce its role in spicule formation and mineralization. To circumvent these problems, we expressed a tag-free bacterial model recombinant spicule matrix protein, rSpSM50. Bioinformatics and biophysical experiments confirm that rSpSM50 is an intrinsically disordered, aggregation-prone C-type lectin-like domain-containing protein that forms dimensionally and internally heterogeneous protein hydrogels that control the in vitro mineralization process in three ways. The hydrogels (1) kinetically stabilize the aqueous calcium carbonate system against nucleation and thermodynamically destabilize the initially formed ACC in bulk solution, (2) promote and organize faceted single-crystal calcite and polycrystalline vaterite nanoparticles, and (3) promote surface texturing of calcite crystals and induce subsurface nanoporosities and channels within both calcite and vaterite crystals. Many of these features are also common to mollusk shell nacre proteins and the sea urchin spicule matrix glycoprotein, SpSM30B/C, and we conclude that rSpSM50 is a spiculogenesis hydrogelator protein that exhibits traits found in other calcium carbonate mineral-modification proteins.

Direct Observation of Nacre Proteins in the Whole Calcite by Super-resolution Microscopy Reveals Diverse Occlusion Patterns

Biominerals are directed by macromolecules, especially proteins, and incorporate organic occlusions contributing to their overall mechanical properties. However, their distribution patterns in biominerals at the microscale are unclear. Here, we labeled nacre proteins of the pearl oyster Pinctada fucata with cyanine 5 and then directly observed their distribution inside the whole synthetic calcite by using stochastic optical reconstruction microscopy (STORM). Compared to traditional microscopy, we found three forms of occlusions in the crystals, i.e., chain-like, islet-like, and haze-like clusters. In addition, in the whole calcite, a two-ring pattern occurred. Based on the images, we studied the crystal growth process in the presence of nacre proteins with an overgrowth experiment. This study provides a novel approach to directly observe the distribution of nacre proteins in the whole calcite, which has implications for understanding the structures and mechanisms of formation of biominerals as well as for...

Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite

Engineering at nanoscale holds the promise of tuning materials with extraordinary properties. However, macroscopic approaches commonly used to predict mechanical properties do not fully apply at nanoscale level. A controversial feature is the presence of nanoflaws in aragonite nacre, as it is expected that flaws would weaken the material, whereas nacre still shows high toughness and rupture strength. Here, we performed molecular dynamics and finite element simulations emulating flaws found in aragonite nacre. Our simulations reveal two regimes for fracture: nacre remains flaw-insensitive only for flaws smaller than 1.2 nm depth, or flaws of a few atoms, whereas larger flaws follow a Griffith-like trend resembling macroscopic fracture. We tested an alternative mechanism for flaw-insensitivity in nacre, and investigated the mechanical effect of organic filling to mitigate fracture. We found that a single nacre protein, perlucin, decreases the stress concentration at the fracture point, producing enhancements of up to 15% in rupture strength. Our study reveals a more comprehensive understanding of mechanical stability at the nanoscale and offers new routes toward hybrid nanomaterials.

Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa.

The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell-forming tissue, the mantle. This so-called 'calcifying matrix' is a complex mixture of proteins, glycoproteins and polysaccharides that is assembled and occluded within the mineral phase during the calcification process. Better molecular-level characterization of the substances that regulate nacre formation is still required. Notable advances in expressed tag sequencing of freshwater mussels, such as Elliptio complanata and Villosa lienosa, provide a pre-requisite to further characterize bivalve nacre proteins by a proteomic approach. In this study, we have identified a total of 48 different proteins from the insoluble matrices of the nacre, 31 of which are common to both E. complanata and V. lienosa A few of these proteins, such as PIF, MSI60, CA, shematrin-like, Kunitz-like, LamG, chitin-binding-containing proteins, together with A-, D-, G-, M- and Q-rich proteins, appear to be analogues, if not true homologues, of proteins previously described from the pearl oyster or the edible mussel nacre matrices, thus forming a remarkable list of deeply conserved nacre proteins. This work constitutes a comprehensive nacre proteomic study of non-pteriomorphid bivalves that has enabled us to describe the molecular basis of a deeply conserved biomineralization toolkit among nacreous shell-bearing bivalves, with regard to proteins associated with other shell microstructures, with those of other mollusc classes (gastropods, cephalopods) and, finally, with other lophotrochozoans (brachiopods).

A Model Sea Urchin Spicule Matrix Protein Self-Associates To Form Mineral-Modifying Protein Hydrogels.

In the purple sea urchin Strongylocentrotus purpuratus, the formation and mineralization of fracture-resistant skeletal elements such as the embryonic spicule require the combinatorial participation of numerous spicule matrix proteins such as the SpSM30A-F isoforms. However, because of limited abundance, it has been difficult to pursue extensive biochemical studies of the SpSM30 proteins and deduce their role in spicule formation and mineralization. To circumvent these problems, we expressed a model recombinant spicule matrix protein, rSpSM30B/C, which possesses the key sequence attributes of isoforms "B" and "C". Our findings indicate that rSpSM30B/C is expressed in insect cells as a single polypeptide containing variations in glycosylation that create microheterogeneity in rSpSM30B/C molecular masses. These post-translational modifications incorporate O- and N-glycans and anionic mono- and bisialylated and mono- and bisulfated monosaccharides on the protein molecules and enhance its aggregation propensity. Bioinformatics and biophysical experiments confirm that rSpSM30B/C is an intrinsically disordered, aggregation-prone protein that forms porous protein hydrogels that control the in vitro mineralization process in three ways: (1) increase the time interval for prenucleation cluster formation and transiently stabilize an ACC polymorph, (2) promote and organize single-crystal calcite nanoparticles, and (3) promote faceted growth and create surface texturing of calcite crystals. These features are also common to mollusk shell nacre proteins, and we conclude that rSpSM30B/C is a spiculogenesis protein that exhibits traits found in other calcium carbonate mineral modification proteins.

Synergistic Biomineralization Phenomena Created by a Combinatorial Nacre Protein Model System.

In the nacre or aragonite layer of the mollusk shell, proteomes that regulate both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets from mineral nanoparticle precursors exist. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights, we have created a proportionally defined combinatorial model consisting of two nacre-associated proteins, C-RING AP7 (shell nacre, Haliotis rufescens) and pseudo-EF hand PFMG1 (oyster pearl nacre, Pinctada fucata), whose individual in vitro mineralization functionalities are well-documented and distinct from one another. Using scanning electron microscopy, flow cell scanning transmission electron microscopy, atomic force microscopy, Ca(II) potentiometric titrations, and quartz crystal microbalance with dissipation monitoring quantitative analyses, we find that both nacre proteins are functionally active within the same mineralization environments and, at 1:1 molar ratios, synergistically create calcium carbonate mesoscale structures with ordered intracrystalline nanoporosities, extensively prolong nucleation times, and introduce an additional nucleation event. Further, these two proteins jointly create nanoscale protein aggregates or phases that under mineralization conditions further assemble into protein-mineral polymer-induced liquid precursor-like phases with enhanced ACC stabilization capabilities, and there is evidence of intermolecular interactions between AP7 and PFMG1 under these conditions. Thus, a combinatorial model system consisting of more than one defined biomineralization protein dramatically changes the outcome of the in vitro biomineralization process.

A nacre protein forms mesoscale hydrogels that “hijack” the biomineralization process within a seawater environment

We examined the mineralization performance of a nacre protein, AP7, within seawater mineralization assays that form aragonite and magnesium calcite. Under these conditions AP7 forms hydrogel particles that vary in size and complexity depending upon ionic conditions. These hydrogels “hijack” the mineralization process by limiting nucleation in bulk solution and promoting nucleation within the hydrogels.

Thermal Stability of Nacre Proteins of the Polynesian Pearl Oyster: A Proteomic Study

Mollusc shells are organic-inorganic composites that are often preserved in the fossil record. However, the way the organic fraction, also called shell matrix, gets fossilized remains an unsolved question, in spite of several old and more recent studies. In the present paper, we have tried to mimic a diagenetic process by constantly heating for ten days at 100°C fresh nacre powder samples of the Polynesian pearl oyster Pinctadamargaritifera. Each day, aliquots of nacre powder were sampled and the matrix was subsequently extracted. It was further analysed by direct weigh quantification, by immunological techniques and by proteomics. Our preliminary data suggest that nacre proteins, when heated at 100°C in dry condition, degrade rather slowly. We evidenced a differential degradation pattern of the soluble and insoluble fractions, and showed that some nacre proteins of the insoluble fraction are stable after ten days of heating. Factors that influence the diagenetic stability of some shell proteins are discussed.

Unveiling the Evolution of Bivalve Nacre Proteins by Shell Proteomics of Unionoidae

The formation of the molluscan shell nacre is regulated to a large extent by a matrix of extracellular macromolecules that are secreted by the shell forming tissue, the mantle. This so called “calcifying matrix” is a complex mixture of proteins and glycoproteins that is assembled and occluded within the mineral phase during the calcification process. While the importance of the calcifying matrix to shell formation has long been appreciated, the molecular basis that dictates nacre formation remains largely uncharacterized.Recent expressed sequence tag (EST) investigations of the freshwater mussels (Elliptio complanata and Villosa leinosa) provide an opportunity to further characterize the proteins in the bivalve shell by a proteomic approach. In this study, we have identified a total of 15 proteins from their nacre insoluble matrices. Few of these proteins, such as Pif, MSI60, Nacrein-like, Shematrin, Kunitz-like containing, Papilin-like, LamG containing, Chitin-binding containing, M-rich and Q-rich proteins, appear to be analogs, if not true homologs, of proteins previously described from the pearl oyster or the edible mussel nacre matrices. This work constitutes a comprehensive EST-based nacre proteomic study of non-pteriomorphid bivalves that concretely gives us the opportunity to describe the molecular basis of deeply conserved nacre biomineralization toolkit within nacreous shell bearing bivalves.

Pif97, a von Willebrand and Peritrophin Biomineralization Protein, Organizes Mineral Nanoparticles and Creates Intracrystalline Nanochambers.

The formation of the mollusk nacre layer involves the assembly and organization of mineral nanoparticles into fracture-toughened mesoscale-sized aragonite tablets that possess intracrystalline nanoporosities. At least one nacre protein family, known as the framework proteome, is strategically located as part of a macromolecular coating around each nacre tablet and is believed to participate in tablet formation. Here, we report new studies of a recombinant form (rPif97) of a unique Japanese pearl oyster (Pinctada fucata) nacre framework biomineralization protein, Pif97. This unique protein possesses both a von Willlebrand factor type A domain (vWA, F23-Y161) and a Peritrophin A chitin-binding domain (PAC, E234-D298). rPif97 self-associates or aggregates to form amorphous protein phases that organize both amorphous and single-crystal calcium carbonate nanoparticles in vitro. Further, in the presence of nucleating calcite crystals, rPif97 protein phases deposit onto these crystals and become occluded over time, forming nanochambers within the crystal interior. The formation of these mineral-modifying amorphous protein phases is linked to the presence of intrinsic disorder and amyloid-like cross-β-strand aggregation-prone regions, and three-dimensional modeling indicates that both the vWA and PAC domains are accessible for intermolecular interactions. Thus, the vWA- and PAC-containing Pif97 protein exhibits key functionalities that would allow its participation in mollusk nacre layer tablet assembly and porosity formation.