Secondary structure and dynamics study of the intrinsically disordered silica‐mineralizing peptide P₅S₃ during silicic acid condensation and silica decondensation

Abstract

The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5S3, a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains five protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2) at globally undersaturated concentrations. The secondary structure of P5S3 during these two processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate. The NMR studies of dual-labeled (13C, 15N) P5S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5 to 9.5 in the absence of silicic acid, the CD data showed a disordered structure with the suggestion of some polyproline II character. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. The secondary structural changes observed for P5S3 correlate with the presence of oligomeric/polymeric silicic acid, presumably due to P5S3-silica interactions. These P5S3-silica interactions appear, at least in part, ionic in nature since negatively charged dodecylsulfate caused similar perturbations to the P5S3 CD spectrum as observed with silica, while uncharged ß-D-dodecyl maltoside did not affect the CD spectrum of P5S3. Thus, with an associated increase in α-helical character, P5S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid.

Quantitative Cooperative Binding Model for Intrinsically Disordered Proteins Interacting with Nanomaterials

“…5 Examples include the interaction of the disordered transactivation domain of the human tumor suppressor p53 (p53TAD) with the globular domain of MDM2 protein, 6 the interaction of the disordered prokaryotic ubiquitin-like protein (Pup) with mycobacterium proteasomal ATPase, 7 and the interaction of disordered silaffin peptides with inorganic silica surfaces. 8 In some cases, these interactions are known to be highly cooperative, 9−11 but the lack of quantitative information at atomic detail has prevented a deeper understanding of such interactions, and the physical−chemical basis for the emergence of cooperativity has remained unaddressed. The hallmark of cooperativity in these systems is that individual residues specifically affect the binding free energy of other residues of the same polypeptide; i.e., the absolute net free energy of binding is generally larger than the sum of the free energy contributions of individual residues.…”

“…Intrinsically disordered proteins (IDPs) and protein regions, which account for more than 30% of the eukaryotic proteome, are involved in a vast range of biologically important processes, such as regulation, catalysis, or biomineralization. − Their high structural flexibility enables IDPs to interact in unique ways with other biomolecules or inorganic materials . Examples include the interaction of the disordered transactivation domain of the human tumor suppressor p53 (p53TAD) with the globular domain of MDM2 protein, the interaction of the disordered prokaryotic ubiquitin-like protein (Pup) with mycobacterium proteasomal ATPase, and the interaction of disordered silaffin peptides with inorganic silica surfaces . In some cases, these interactions are known to be highly cooperative, − but the lack of quantitative information at atomic detail has prevented a deeper understanding of such interactions, and the physical–chemical basis for the emergence of cooperativity has remained unaddressed.…”