Manifold of self-assembly of a de novo designed peptide: amyloid fibrils, peptide bundles, and fractals.

We report that a peptide with the sequence of EGAGAAAAGAGE can have different aggregation states, viz., amyloid fibrils, peptide bundles, and fractal assembly under different incubation conditions. The chemical state of the Glu residue played a pivotal regulating role in the aggregation behavior of the peptide. The mechanism of the fractal assembly of this peptide has been unraveled as follows. The peptide fragments adopting the beta-sheet conformation are well dispersed in alkaline solution. In the buffer of sodium bicarbonate, peptide rods are formed with considerable structural rigidity at the C- and N-termini. The peptide rods undergo random trajectory in the solution and form a fractal pattern on a two-dimensional surface via the diffusion-limited aggregation process.

Kinetics of the simplest Criegee intermediate reaction with ozone studied using a mid-infrared quantum cascade laser spectrometer.

The kinetics of the reaction of CH2OO with ozone has been studied by monitoring CH2OO using time-resolved infrared (IR) absorption spectroscopy, which utilized the fast chirped IR pulse train from a quantum cascade laser [J. Chem. Phys., 2017, 146, 244302]. CH2OO was prepared by photolyzing a gas mixture of CH2I2/O2/O3 at 352 nm; the photolysis wavelength was chosen to minimize the photodissociation of O3. The measured rate coefficient at 298 K and 30 Torr is (6.7 ± 0.5) × 10-14 cm3 s-1, independent of pressure from 30 to 100 Torr. The result indicates that previous ab initio calculations either underestimated or overestimated this reaction rate by one order of magnitude or more. The result also implies that, the reaction of the Criegee intermediate with ozone may play a role in laboratory studies of ozonolysis of alkenes. However, this reaction would not compete with other CH2OO sinks in the atmosphere.

High resolution quantum cascade laser spectroscopy of the simplest Criegee intermediate, CH2OO, between 1273 cm-1 and 1290 cm-1.

The region 1273-1290 cm-1 of the ν4 fundamental of the simplest Criegee intermediate, CH2OO, has been measured using a quantum cascade laser transient absorption spectrometer, which offers greater sensitivity and spectral resolution (<0.004 cm-1) than previous works based on thermal light sources. Gas phase CH2OO was generated from the reaction of CH2I + O2 at 298 K and 4 Torr. The analysis of the absorption spectrum has provided precise values for the vibrational frequency and the rotational constants, with fitting errors of a few MHz. The determined ratios of the rotational constants, A'/A″ = 0.9986, B'/B″ = 0.9974, and C'/C″ = 1.0010, and the relative intensities of the a- and b-type transitions, 90:10, are in good agreement with literature values from a theoretical calculation using the MULTIMODE approach, based on a high-level ab initio potential energy surface. The low-K (=Ka) lines can be fitted extremely well, but rotational perturbations by other vibrational modes disrupt the structure for K = 4 and K ≥ 6. Not only the spectral resolution but also the detection sensitivity of CH2OO IR transitions has been greatly improved in this work, allowing for unambiguous monitoring of CH2OO in kinetic studies at low concentrations.

Structural characterization of fluoride species in shark teeth.

In shark teeth we have identified the species fluorapatite, hydroxyfluorapatite and its defect site, calcium fluoride, and potassium fluoride. Their relative amounts in teeth at different development stages have been quantified. Calcium fluoride and potassium fluoride may be associated with the fluoridation mechanism in shark teeth.

Is Mg-stabilized amorphous calcium carbonate a homogeneous mixture of amorphous magnesium carbonate and amorphous calcium carbonate?

We find two types of carbonate ions in Mg stabilized amorphous calcium carbonate (Mg-ACC), whose short-range orders are identical to those of ACC and amorphous magnesium carbonate (AMC). Mg-ACC comprises a homogeneous mixture of the nano-clusters of ACC and AMC. Their relative amount varies systematically at different pH.

Study of Binding Interaction between Pif80 Protein Fragment and Aragonite.

Pif is a crucial protein for the formation of the nacreous layer in Pinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of ß-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization.

Purification of recombinant nacre-associated mineralization protein AP7 fused with maltose-binding protein.

Formation of biominerals often involves specific proteins that modulate the process of matrix assembly, nucleation, and crystal growth. AP7 is an aragonite-associated protein of 7 kDa and is intrinsically disordered. The structural disorder of AP7 makes it very difficult to express in Escherchiacoli. In this work, we report the first successful expression and purification of recombinant AP7 using the maltose-binding protein (MBP) fusion approach. We obtain a high-yield production of recombinant MBP-AP7 protein inE. coli (∼60 mg/L). We also establish an efficient protocol to remove the MBP fusion protein by Factor Xa, followed by purification using size-exclusion chromatography. Characterization of the recombinant AP7 protein has been carried out using MALDI-TOF, peptide mass fingerprinting, and circular dichroism (CD). The mass data confirm that the purified recombinant protein is AP7. The CD data suggest that the recombinant AP7 protein exists as partially disordered structure at neutral pH. The calcium carbonate precipitation assay shows that both MBP-AP7 and AP7 exhibit morphological modification on calcite crystallites. The co-precipitation of MBP-tagged AP7 derivatives and calcium carbonate generate different types of AP7 composite calcite and vaterite crystals. This system should be helpful to establish a model for understanding the structure/function relationship between the protein and inorganic mineral interaction.