Motivation: The formation of aragonite mineral in the mollusk shell or pearl nacre requires the participation of a diverse set of proteins that form the mineralized extracellular matrix. Although self-assembly processes have been identified for several nacre proteins, these proteins do not contain known globular protein–protein binding domains. Thus, we hypothesize that other sequence features are responsible for nacre matrix protein–protein assembly processes and ultimately aragonite biosynthesis. Results: Of 39 mollusk aragonite-associated protein sequences, 100% contain at least one region of intrinsic disorder or unfolding, with the highest percentages found in framework and pearl-associated proteins relative to the intracrystalline proteins. In some instances, these intrinsically disordered regions were identified as bind/fold sequences, and a limited number correlate with known biomineral-relevant sequences. Interestingly, 95% of the aragonite-associated protein sequences were found to contain at least one occurrence of amyloid-like or cross-β strand aggregation-prone supersecondary motifs, and this correlates with known aggregation and aragonite formation functions in three experimentally tested protein sequences. Collectively, our findings indicate that aragonite-associated proteins have evolved signature sequence traits of intrinsic disorder and aggregation-prone regions that are important for their role(s) in matrix assembly and mineralization. Contact:jse1@nyu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Over the past several decades, numerous studies have attempted to define the general role that proteins play in the nucleation of biominerals in organisms. Recently, with the emergence of the non-classical nucleation scheme involving pre-nucleation cluster formation, amorphous mineral cluster assembly, and maturation/stabilization scenarios, there is a growing realization that proteins could efficiently regulate many steps in this process, resulting in precise control over the development of biogenic crystals or the indefinite stabilization of amorphous mineral phases in a wide variety of organisms. In this Highlight, we present a generic scheme where nucleation-specific biomineralization proteins containing intrinsically disordered and aggregation-prone sequences assemble to form a liquid- or fluid-like phase similar to that formed in the polymer-induced liquid phase (PILP) and in vitro liquid protein systems. This assembled protein phase is compatible with the physical-chemical properties of prenucleation clusters and amorphous mineral clusters, and can provide an environment for subsequent stabilization and/or transformation of the mineral phase under appropriate conditions and locations. We foresee some important applications arising from Nature's use of protein assemblies to create, stabilize, and transform amorphous mineral precursor phases.