Ashit Rao

A Nacre Protein, n16.3, Self-Assembles To Form Protein Oligomers That Dimensionally Limit and Organize Mineral Deposits

The mollusk shell is a complex biological material that integrates mineral phases with organic macromolecular components such as proteins. The role of proteins in the formation of the nacre layer (aragonite mineral phase) is poorly understood, particularly with regard to the organization of mineral deposits within the protein extracellular matrix and the identification of which proteins are responsible for this task. We report new experiments that provide insight into the role of the framework nacre protein, n16.3 (Pinctada fucata), as an organizer or assembler of calcium carbonate mineral clusters. Using a combination of biophysical techniques, we find that recombinant n16.3 (r-n16.3) oligomerizes to form amorphous protein films and particles that possess regions of disorder and mobility. These supramolecular assemblies possess an intrinsically disordered C-terminal region (T64-W98) and reorganize in the presence of Ca(2+) ions to form clustered protein oligomers. This Ca(2+)-induced reorganization leads to alterations in the molecular environments of Trp residues, the majority of which reside in putative aggregation-prone cross-β strand regions. Potentiometric Ca(2+) titrations reveal that r-n16.3 does not significantly affect the formation of prenucleation clusters in solution, and this suggests a role for this protein in postnucleation mineralization events. This is verified in subsequent in vitro mineralization assays in which r-n16.3 demonstrates its ability to form gel-like protein phases that organize and cluster nanometer-sized single-crystal calcite relative to protein-deficient controls. We conclude that the n16 nacre framework proteome creates a protein gel matrix that organizes and dimensionally limits mineral deposits. This process is highly relevant to the formation of ordered, nanometer-sized nacre tablets in the mollusk shell.

Roles of larval sea urchin spicule SM50 domains in organic matrix self-assembly and calcium carbonate mineralization

The larval spicule matrix protein SM50 is the most abundant occluded matrix protein present in the mineralized larval sea urchin spicule. Recent evidence implicates SM50 in the stabilization of amorphous calcium carbonate (ACC). Here, we investigate the molecular interactions of SM50 and CaCO3 by investigating the function of three major domains of SM50 as small ubiquitin-like modifier (SUMO) fusion proteins - a C-type lectin domain (CTL), a glycine rich region (GRR) and a proline rich region (PRR). Under various mineralization conditions, we find that SUMO-CTL is monomeric and influences CaCO3 mineralization, SUMO-GRR aggregates into large protein superstructures and SUMO-PRR modifies the early CaCO3 mineralization stages as well as growth. The combination of these mineralization and self-assembly properties of the major domains synergistically enable the full-length SM50 to fulfill functions of constructing the organic spicule matrix as well as performing necessary mineralization activities such as Ca(2+) ion recruitment and organization to allow for proper growth and development of the mineralized larval sea urchin spicule.

An Oligomeric C-RING Nacre Protein Influences Prenucleation Events and Organizes Mineral Nanoparticles

The mollusk shell nacre layer integrates mineral phases with macromolecular components such as intracrystalline proteins. However, the roles performed by intracrystalline proteins in calcium carbonate nucleation and subsequent postnucleation events (e.g., organization of mineral deposits) in the nacre layer are not known. We find that AP7, a nacre intracrystalline C-RING protein, self-assembles to form amorphous protein oligomers and films on mica that further assemble into larger aggregates or phases in the presence of Ca2+. Using solution nuclear magnetic resonance spectroscopy, we determine that the protein assemblies are stabilized by interdomain interactions involving the aggregation-prone T31-N66 C-terminal C-RING domain but are destabilized by the labile nature of the intrinsically disordered D1-T19 AA N-terminal sequence. Thus, the dynamic, amorphous nature of the AP7 assemblies can be traced to the molecular behavior of the N-terminal sequence. Using potentiometric methods, we observe that AP7 protein phases prolong the time interval for prenucleation cluster formation but neither stabilize nor destabilize ACC clusters. Time-resolved flow cell scanning transmission electron microscopy mineralization studies confirm that AP7 protein phases delay the onset of nucleation and assemble and organize mineral nanoparticles into ring-shaped branching clusters in solution. These phenomena are not observed in protein-deficient assays. We conclude that C-RING AP7 protein phases modulate the time period for early events in nucleation and form strategic associations with forming mineral nanoparticles that lead to mineral organization.

Insect Cell Glycosylation and Its Impact on the Functionality of a Recombinant Intracrystalline Nacre Protein, AP24

The impacts of glycosylation on biomineralization protein function are largely unknown. This is certainly true for the mollusk shell, where glycosylated intracrystalline proteins such as AP24 (Haliotis rufescens) exist but their functions and the role of glycosylation remain elusive. To assess the effect of glycosylation on protein function, we expressed two recombinant variants of AP24: an unglycosylated bacteria-expressed version (rAP24N) and a glycosylated insect cell-expressed version (rAP24G). Our findings indicate that rAP24G is expressed as a single polypeptide containing variations in glycosylation that create microheterogeneity in rAP24G molecular masses. These post-translational modifications incorporate O- and N-glycans and anionic monosialylated and bisialylated, and monosulfated and bisulfated monosaccharides on the protein molecules. AFM and DLS experiments confirm that both rAP24N and rAP24G aggregate to form protein phases, with rAP24N exhibiting a higher degree of aggregation, compared to rAP24G. With regard to functionality, we observe that both recombinant proteins exhibit similar behavior within in vitro calcium carbonate mineralization assays and potentiometric titrations. However, rAP24G modifies crystal growth directions and is a stronger nucleation inhibitor, whereas rAP24N exhibits higher mineral phase stabilization and nanoparticle containment. We believe that the post-translational addition of anionic groups (via sialylation and sulfation), along with modifications to the protein surface topology, may explain the changes in glycosylated rAP24G aggregation and mineralization behavior, relative to rAP24N.

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.

On the biophysical regulation of mineral growth: Standing out from the crowd

Biogenic mineralization processes are generally regulated by soluble additives and insoluble matrices. This endows precise control over the different stages of mineralization such as the uptake, transport of mineral precursors as well as the subsequent deposition of the mineral phases with consistent compositions and morphologies. Programmed in the interactions of organic molecules with different precursor species and the fine modulation of the niche environments, a formative elegance is reflected in the biological means for crystal formation in comparison to the synthetic counterparts. In order to spotlight the role of prevalent biophysical environments in the emergence of fascinating materials, we revisit biologically modulated mineralization to describe nucleation and crystallization under physicochemical highly non-ideal conditions on account of macromolecular crowding and the gel-like nature of cellular matrices.

Mineralization Schemes in the Living World: Mesocrystals

With the expanding knowledge on structure–property relations in biogenic minerals, an emerging challenge is to decipher the underlying biochemical and physical mechanisms of material formation. For this purpose, the dependence of spatial properties of minerals including composition, structure, and orientation on dynamic processes such as the transport of mineral precursors as well as the nucleation and growth of particles requires elucidation. The aim of this chapter is to provide an overview of biomineralization processes in light of the nonclassical pathways of nucleation and crystallization. We address the mechanistic emergence of mesocrystallinity among diverse biomineral architectures as well as the associated checkpoints regulating particle nucleation, growth, and assembly.

Calcium carbonate crystallization in tailored constrained environments

Synthesis of inorganic particles using routes inspired by biomineralization is a goal of growing interest. Recently it was demonstrated that the size and geometry of crystallization sites are as important as the structure of charged templating surfaces to obtain particles with controlled features. Most biominerals are formed inside restricted, constrained or confined spaces where at least parts of the boundaries are cell membranes containing phospholipids. In this study, we used a gas diffusion method to determine the effect of different lecithin media on the crystallization of CaCO3 and to evaluate the influence of the spatial arrangement of lecithin molecules on templating CaCO3 crystal formation. By using inorganic synthesis, Raman spectroscopy, dynamic light scattering, electrochemical methods and scanning electron microscopy, we showed that the occurrence of surface-modified calcite crystals and diverse textured vaterite crystals reflects the geometry and spatial distribution of aqueous constrained spaces due to the lecithin assembly controlled by lecithin concentration in an ionized calcium chloride solution under a continuous CO2 diffusion atmosphere. This research shows that by tailoring the assembly of lecithin molecules, as micelles or reversed micelles, it is possible to modulate the texture, polymorphism, size and shape of calcium carbonate crystals.

Morphology control and molecular templates in biomineralization

Abstract Several materials in the biological world incorporate structural complexities such as intricate morphology, hierarchical organization as well as sophisticated organic–inorganic interfaces that lead to the subsequent emergence of superior physical properties. Such materials are designed by Nature for specialized functions. On an evolutionary timescale, organisms producing these biomaterials can have certain survival advantages against hostile growth conditions and predation ( Kunkel et al., 2012 ). Moreover, considering the vastness of biological diversity and the presence of life at different conditions of temperature and pressure, the diverse physical properties as well as the mechanisms underlying the formation of these materials are evolutionarily optimized by Nature. Therefore elucidating the mechanisms of formation and structural details of biomaterials as well as their role in the emergence of physical properties is highly relevant ( Mann, 1993 , Mann, 1997 , Meldrum and Colfen, 2008 , Lowenstam and Weiner, 1989 , Mann and Ozin, 1996 , Bensaude-Vincent et al., 2002 ). This book chapter introduces a class of biomaterials, i.e., biominerals, and their fascinating architectures. Furthermore, the growth mechanisms and complex morphologies of biominerals are addressed in light of recent developments in the understanding of crystal nucleation and growth.

Crystallization and preliminary X-ray analysis of the C-type lectin domain of the spicule matrix protein SM50 from Strongylocentrotus purpuratus

Sea urchin spicules have a calcitic mesocrystalline architecture that is closely associated with a matrix of proteins and amorphous minerals. The mechanism underlying spicule formation involves complex processes encompassing spatio-temporally regulated organic-inorganic interactions. C-type lectin domains are present in several spicule matrix proteins in Strongylocentrotus purpuratus, implying their role in spiculogenesis. In this study, the C-type lectin domain of SM50 was overexpressed, purified and crystallized using a vapour-diffusion method. The crystal diffracted to a resolution of 2.85 Å and belonged to space group P212121, with unit-cell parameters a = 100.6, b = 115.4, c = 130.6 Å, α = β = γ = 90°. Assuming 50% solvent content, six chains are expected to be present in the asymmetric unit.