Molecular dynamics insights into biomineralisation mediated by acidic intrinsically disordered proteins: a case study of molluscan Aspein from the pearl oyster Pinctada fucata

Abstract

Biomineralisation is a ubiquitous phenomenon that still fascinates the scientific community. Mineralised structures are most notably encountered in marine lifeforms the shell or exoskeleton of which are formed by precipitating specific calcium carbonate (CaCO3) polymorphs, known as amorphous (ACC), vaterite, aragonite, and calcite. To control crystalline polymorphism in their shell layers, bivalves have evolved strategies involving ion-binding secretomes composed of shell matrix proteins (SMPs). Secreted in the prismatic layer of the pearl oyster Pinctada fucata, Aspein is an unusually acid-rich protein exclusively aspartic and famously recognised as the most acidic SMP known to date. Through in vitro crystallisation experiments, Aspein was shown to select calcite over aragonite in modern seawater conditions. However, how it exerts its selectivity with respect to its structural properties remains enigmatic. By combining sequence-based predictions with all-atom molecular dynamics simulations, we unveiled that Aspein is an intrinsically disordered organic matrix protein (IDOMP) undergoing ion-specific chain collapse and phase separation. Thanks to its unique Asp density and conformational fuzziness, Aspein first sequesters Ca2+ then attracts CO32- ions before stabilising ACC and calcite-like phases, while precluding the incorporation of Mg2+ to avoid aragonite formation. Indeed, via Asp-Ca2+ bridges, structure-less clusters coalescence into supersaturated protein-CaCO3 assemblies initiates calcite crystallisation. Therefore, Aspein plasticity, condensation susceptibility, and aspartic density critically modulate the pathway that defines CaCO3 polymorphism by inhibiting nucleation and controlling the growth of biogenic minerals. From a broader perspective, our study underpins some of the molecular and physico-chemical principles governing biomineralisation processes mediated by IDOMPs, the overlooked, yet prevalent, role of which was mechanistically unexplored.