Understanding the Dynamic Aggregation in Single-Atom Catalysis.

The dynamic response of single-atom catalysts to a reactive environment is an increasingly significant topic for understanding the reaction mechanism at the molecular level. In particular, single atoms may experience dynamic aggregation into clusters or nanoparticles driven by thermodynamic or kinetic factors. Herein, the inherent mechanistic nuances that determine the dynamic profile during the reaction will be uncovered, including the intrinsic stability and site-migration barrier of single atoms, external stimuli (temperature, voltage, and adsorbates), and the influence of catalyst support. Such dynamic aggregation can be beneficial or deleterious on the catalytic performance depending on the optimal initial state. Those examples will be highlighted where in situ formed clusters, rather than single atoms, serve as catalytically active sites for improved catalytic performance. This is followed by the introduction of operando techniques to understand the structural evolution. Finally, the emerging strategies via confinement and defect-engineering to regulate dynamic aggregation will be briefly discussed.

Goldilocks Energy Minimum: Peptide-Based Reversible Aggregation and Biosensing.

Colorimetric biosensors based on gold nanoparticle (AuNP) aggregation are often challenged by matrix interference in biofluids, poor specificity, and limited utility with clinical samples. Here, we propose a peptide-driven nanoscale disassembly approach, where AuNP aggregates induced by electrostatic attractions are dissociated in response to proteolytic cleavage. Initially, citrate-coated AuNPs were assembled via a short cationic peptide (RRK) and characterized by experiments and simulations. The dissociation peptides were then used to reversibly dissociate the AuNP aggregates as a function of target protease detection, i.e., main protease (Mpro), a biomarker for severe acute respiratory syndrome coronavirus 2. The dissociation propensity depends on peptide length, hydrophilicity, charge, and ligand architecture. Finally, our dissociation strategy provides a rapid and distinct optical signal through Mpro cleavage with a detection limit of 12.3 nM in saliva. Our dissociation peptide effectively dissociates plasmonic assemblies in diverse matrices including 100% human saliva, urine, plasma, and seawater, as well as other types of plasmonic nanoparticles such as silver. Our peptide-enabled dissociation platform provides a simple, matrix-insensitive, and versatile method for protease sensing.

Nano-size dependent protein corona formation by SARS-CoV-2 Omicron spike protein over gold nano-colloid and reversible aggregation.

The adsorption process of SARS-CoV-2 Omicron spike protein to the nano-gold colloid surfaces was examined by monitoring the surface plasmon resonance (SPR) band shift of gold-nano particles ranging between diameters of d = 10-100 nm. The externally changed pH between 3 and 11 at 24.5 ± 0.4 °C initiated a reversible formation of the gold colloid aggregates, where formation/deformation of the aggregates were monitored by red/blue shift of the peak of the SPR band. There was no sign of reversible aggregation for d = 10, 15, and 20 nm gold colloids. A clear undulation of the peak shift corresponding to pH hopping between pH ~3 and ~11 was confirmed for colloidal d > 30 nm. This degree of the reversibility was compared to previously reported SARS-CoV-2 Alpha spike protein coated gold colloids. It was concluded that Omicron spike protein possesses a similar low affinity for gold nano particle d < 20 nm and possesses the higher affinity to the gold nanoparticles of d > 30 nm. However, the Omicron spike protein conformation was presumed to be more denatured compared to the SARS-CoV-2 Alpha spike protein. Our finding suggested Omicron spike protein was more acid labile/flexible.

Yeast Proteins may Reversibly Aggregate like Amphiphilic Molecules.

More than a hundred proteins in yeast reversibly aggregate and phase-separate in response to various stressors, such as nutrient depletion and heat shock. We know little about the protein sequence and structural features behind this ability, which has not been characterized on a proteome-wide level. To identify the distinctive features of aggregation-prone protein regions, we apply machine learning algorithms to genome-scale limited proteolysis-mass spectrometry (LiP-MS) data from yeast proteins. LiP-MS data reveals that 96 proteins show significant structural changes upon heat shock. We find that in these proteins the propensity to phase separate cannot be solely driven by disordered regions, because their aggregation-prone regions (APRs) are not significantly disordered. Instead, the phase separation of these proteins requires contributions from both disordered and structured regions. APRs are significantly enriched in aliphatic residues and depleted in positively charged amino acids. Aggregator proteins with longer APRs show a greater propensity to aggregate, a relationship that can be explained by equilibrium statistical thermodynamics. Altogether, our observations suggest that proteome-wide reversible protein aggregation is mediated by sequence-encoded properties. We propose that aggregating proteins resemble supra-molecular amphiphiles, where APRs are the hydrophobic parts, and non-APRs are the hydrophilic parts.

Study on the Mechanism of the Reversible Color Change of Polyacrylic Acid Modified Gold Nanoparticles Responding to pH.

In view of various explanations regarding the pH response of the nanocomposite of gold nanoparticles (AuNPs) modified with polyacrylic acid (PAA) molecules in reported literature, in this work, AuNPs with a size of 20 nm saturatedly loaded with PAA molecules (AuNPs-PAAs) were used to investigate the following aspects of this issue. We investigated the effects of pH on the stability of AuNPs-PAAs in the presence of salt, CTAB, poly (sodium styrenesulfonate) (PSS), ethanol, and free PAA, respectively. Common techniques were undertaken to evaluate the stability, including UV-Vis spectroscopy, Zeta potential analysis, and TEM. The results show that AuNPs-PAAs could respond to pH variations, having a reversible aggregation-to-disaggregation, accompanying their Zeta potential change. The proposed corresponding mechanism was that this reversible change was attributes to the net charge variation of AuNPs-PAAs induced by a reversible protonation-to-deprotonation of PAA rather than the conformational change. It was found that salt, CTAB, PSS, and free PAA could strengthen the dispersity of AuNPs-PAAs, even though their absolute Zeta potential values were decreased to small values or dropped to nearly zero. This abnormal phenomenon was explained by solvation. It was also found that AuNPs-PAAs have an opposite pH response in aqueous and ethanol solutions, justifying the solvation effect. All these results revealed the conformational stability of PAAs immobilized on AuNPs. The methods and the findings of this investigation give some new insights to understand the pH-response of AuNPs-PAAs composites and the design of AuNPs-PAAs-based functional sensors.

Designing disorder: Tales of the unexpected tails.

Protein tags of various sizes and shapes catalyze progress in biosciences. Well-folded tags can serve to solubilize proteins. Small, unfolded, peptide-like tags have become invaluable tools for protein purification as well as protein-protein interaction studies. Intrinsically Disordered Proteins (IDPs), which lack unique 3D structures, received exponentially increasing attention during the last decade. Recently, large ID tags have been developed to solubilize proteins and to engineer the pharmacological properties of protein and peptide pharmaceuticals. Here, we contrast the complementary benefits and applications of both folded and ID tags based on predictions of ID. Less structure often means more function in a shorter tag.