Skeletal development in the sea urchin relies upon protein families that contain intrinsic disorder, aggregation-prone, and conserved globular interactive domains.

Martin Pendola,Gaurav Jain,John Spencer Evans,Eugene A Permyakov

doi:10.1371/journal.pone.0222068

Abstract

The formation of the sea urchin spicule skeleton requires the participation of hydrogel-forming protein families that regulate mineral nucleation and nanoparticle assembly processes that give rise to the spicule. However, the structure and molecular behavior of these proteins is not well established, and thus our ability to understand this process is hampered. We embarked on a study of sea urchin spicule proteins using a combination of biophysical and bioinformatics techniques. Our biophysical findings indicate that recombinant variants of the two most studied spicule matrix proteins, SpSM50 and SpSM30B/C (S. purpuratus) have a conformational landscape that include a C-terminal random coil/intrinsically disordered MAPQG sequence coupled to a conserved, folded N-terminal C-type lectin-like (CTLL) domain, with SpSM50 > SpSM30B/C with regard to intrinsic disorder. Both proteins possess solvent-accessible unfolded MAQPG sequence regions where Asn, Gln, and Arg residues may be accessible for protein hydrogel interactions with water molecules. Our bioinformatics study included seven other spicule matrix proteins where we note similarities between these proteins and rare, unusual proteins that possess folded and unfolded traits. Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive. Collectively these reactive domains would be capable of driving protein assembly and hydrogel formation. Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains. These variations may reflect species-specific requirements for spiculogenesis. We conclude that the molecular landscape of spicule matrix protein families enables them to function as hydrogelators, nucleators, and assemblers of mineral nanoparticles.

Highlights

The formation of endo- and exoskeletons requires the participation of protein families that enable the construction of biomaterials that can withstand stress and provide support, protection, and survival [1,2,3]
Bioinformatics have indicated that SpSM30B/C and SpSM50 proteins contain a folded C-type lectin-like (CTLL) domain at the N-terminus and an unfolded, MAQPG repetitive sequence domain at the C-terminus [13,14]
We find that in the suspended gel state recombinant Strongylocentrotus purpuratus spicule matrix protein SpSM50 (rSpSM50) presents with a single (-) π– π transition minima band centered near 222 nm, and rSpSM30B/C-G exhibits with a single (-) π– π transition minima band centered near 216 nm, i.e., a 6 nm blue shift from rSpSM50

Summary

Introduction

The formation of endo- and exoskeletons requires the participation of protein families that enable the construction of biomaterials that can withstand stress and provide support, protection, and survival [1,2,3]. The idea was to extend our SpSM50 and SpSM30B/C experimental investigations, by using predictive bioinformatics [25,26,27;30,31,32;37,38] to determine the presence of hydrogelator-related structural traits, such as intrinsic disorder, aggregation propensity, and interactive conserved folded sequence regions [13,14] within other spicule matrix proteins. Together, these approaches revealed that spicule matrix protein families have a common molecular landscape that features an open global conformation consisting of intrinsically disordered, amyloid-like cross-beta strand, and folded protein-protein interactive domains.

Results

Discussion

Evans JS The biomineralization proteome