Probing Specificity of Protein-Protein Interactions with Chiral Plasmonic Nanostructures

Ultrasensitive Raman Detection of Biomolecular Conformation at the Attomole Scale using Chiral Nanophotonics

Understanding the function of a biomolecule hinges on its 3D conformation or secondary structure. Chirally sensitive, optically active techniques based on the differential absorption of UV-vis circularly polarized light excel at rapid characterisation of secondary structures. However, Raman spectroscopy, a powerful method for determining the structure of simple molecules, has limited capacity for structural analysis of biomolecules because of intrinsically weak optical activity, necessitating millimolar (mM) sample quantities. A breakthrough is presented for utilising Raman spectroscopy in ultrasensitive biomolecular conformation detection, surpassing conventional Raman optical activity by 15 orders of magnitude. This strategy combines chiral plasmonic metasurfaces with achiral molecular Raman reporters and enables the detection of different conformations (α-helix and random coil) of a model peptide (poly-L/D-lysine) at the ≤attomole level (monolayer). This exceptional sensitivity stems from the ability to detect local, molecular-scale changes in the electromagnetic (EM) environment of a chiral nanocavity induced by the presence of biomolecules using molecular Raman reporters. Further signal enhancement is achieved by incorporating achiral Au nanoparticles. The introduction of the nanoparticles creates highly localized regions of extreme optical chirality. This approach, which exploits Raman, a generic phenomenon, paves the way for next-generation technologies for the ultrasensitive detection of diverse biomolecular structures.

Reshaping and induction of optical activity in gold@silver nanocuboids by chiral glutathione molecules

Core-shell gold-silver cuboidal nanoparticles were produced, with either concave or straight facets. Their incubation with a low concentration of chiral l-glutathione (GSH) biomolecules was found to produce near UV plasmonic extinction and induced circular dichroism (CD) peaks. The effect is sensitive to the silver shell thickness. The GSH molecules were found to cause redistribution of silver in the shell, removing silver atoms from edges/corners and re-depositing them at the nanocuboid facets, probably through some redox and complexation processes between the silver and thiol group of the GSH. Other thiolated chiral biomolecules (and drug molecules) did not show this effect. The emerging near UV surface plasmon resonance is a silver slab resonance, which might also possess some multipolar resonance nature. The concave-shaped nanocuboids exhibited stronger induced plasmonic CD relative to the nanocuboids with straight facets.

Identification of Relevant Protein Interactions with Partial Knowledge: A Complex Network and Deep Learning Approach

Protein-protein interactions (PPIs) are the basis for understanding most cellular events in biological systems. Several experimental methods, e.g., biochemical, molecular, and genetic methods, have been used to identify protein-protein associations. However, some of them, such as mass spectrometry, are time-consuming and expensive. Machine learning (ML) techniques have been widely used to characterize PPIs, increasing the number of proteins analyzed simultaneously and optimizing time and resources for identifying and predicting protein-protein functional linkages. Previous ML approaches have focused on well-known networks or specific targets but not on identifying relevant proteins with partial or null knowledge of the interaction networks. The proposed approach aims to generate a relevant protein sequence based on bidirectional Long-Short Term Memory (LSTM) with partial knowledge of interactions. The general framework comprises conducting a scale-free and fractal complex network analysis. The outcome of these analyses is then used to fine-tune the fractal method for the vital protein extraction of PPI networks. The results show that several PPI networks are self-similar or fractal, but that both features cannot coexist. The generated protein sequences (by the bidirectional LSTM) also contain an average of 39.5% of proteins in the original sequence. The average length of the generated sequences was 17% of the original one. Finally, 95% of the generated sequences were true.

Local Growth Mediated by Plasmonic Hot Carriers: Chirality from Achiral Nanocrystals Using Circularly Polarized Light

Plasmonic nanocrystals and their assemblies are excellent tools to create functional systems, including systems with strong chiral optical responses. Here we study the possibility of growing chiral plasmonic nanocrystals from strictly nonchiral seeds of different types by using circularly polarized light as the chirality-inducing mechanism. We present a novel theoretical methodology that simulates realistic nonlinear and inhomogeneous photogrowth processes in plasmonic nanocrystals, mediated by the excitation of hot carriers that can drive surface chemistry. We show the strongly anisotropic and chiral growth of oriented nanocrystals with lowered symmetry, with the striking feature that such chiral growth can appear even for nanocrystals with subwavelength sizes. Furthermore, we show that the chiral growth of nanocrystals in solution is fundamentally challenging. This work explores new ways of growing monolithic chiral plasmonic nanostructures and can be useful for the development of plasmonic photocatalysis and fabrication technologies.

Nanophotonic Approaches for Chirality Sensing

Chiral nanophotonic materials are promising candidates for biosensing applications because they focus light into nanometer dimensions, increasing their sensitivity to the molecular signatures of their surroundings. Recent advances in nanomaterial-enhanced chirality sensing provide detection limits as low as attomolar concentrations (10^-18 M) for biomolecules and are relevant to the pharmaceutical industry, forensic drug testing, and medical applications that require high sensitivity. Here, we review the development of chiral nanomaterials and their application for detecting biomolecules, supramolecular structures, and other environmental stimuli. We discuss superchiral near-field generation in both dielectric and plasmonic metamaterials that are composed of chiral or achiral nanostructure arrays. These materials are also applicable for enhancing chiroptical signals from biomolecules. We review the plasmon-coupled circular dichroism mechanism observed for plasmonic nanoparticles and discuss how hotspot-enhanced plasmon-coupled circular dichroism applies to biosensing. We then review single-particle spectroscopic methods for achieving the ultimate goal of single-molecule chirality sensing. Finally, we discuss future outlooks of nanophotonic chiral systems.

Superchiral near fields detect virus structure

Optical spectroscopy can be used to quickly characterise the structural properties of individual molecules. However, it cannot be applied to biological assemblies because light is generally blind to the spatial distribution of the component molecules. This insensitivity arises from the mismatch in length scales between the assemblies (a few tens of nm) and the wavelength of light required to excite chromophores (≥150 nm). Consequently, with conventional spectroscopy, ordered assemblies, such as the icosahedral capsids of viruses, appear to be indistinguishable isotropic spherical objects. This limits potential routes to rapid high-throughput portable detection appropriate for point-of-care diagnostics. Here, we demonstrate that chiral electromagnetic (EM) near fields, which have both enhanced chiral asymmetry (referred to as superchirality) and subwavelength spatial localisation (∼10 nm), can detect the icosahedral structure of virus capsids. Thus, they can detect both the presence and relative orientation of a bound virus capsid. To illustrate the potential uses of the exquisite structural sensitivity of subwavelength superchiral fields, we have used them to successfully detect virus particles in the complex milieu of blood serum.

Plasmonic metamaterials for chiral sensing applications

Plasmonic metamaterials are artificially designed materials which exhibit optical properties that cannot be found in nature. They have unique and special abilities related to electromagnetic wave control, including strong field enhancement in the vicinity of the surfaces. Over the years, scientists have succeeded in dramatically improving the detection limit of molecular chirality utilizing a variety of plasmonic metamaterial platforms. In this mini-review, we will discuss the principles of most recent issues in chiral sensing applications of plasmonic metamaterials, including suggested formulas for signal enhancement of chiroptical plasmonic sensors, and studies on various platforms that employ different sensing mechanisms.