SOMSpec as a general purpose validated self-organising map tool for rapid protein secondary structure prediction from infrared absorbance data

A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm−1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

Gold nanoparticles have the potential to be used in biomedical applications from diagnostics to drug delivery. However, interactions of gold nanoparticles with different biomolecules in the cellular environment result in the formation of a “protein corona”—a layer of protein formed around a nanoparticle, which induces changes in the properties of nanoparticles. In this work we developed methods to reproducibly synthesize spheroidal and star-shaped gold nanoparticles, and carried out a physico-chemical characterization of synthesized anionic gold nanospheroids and gold nanostars through transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential (ZP), nanoparticles tracking analysis (NTA), ultraviolet-visible (UV–Vis) spectroscopy and estimates of surface-enhanced Raman spectroscopy (SERS) signal enhancement ability. We analyzed how they interact with proteins after pre-incubation with bovine serum albumin (BSA) via UV–Vis, DLS, ZP, NTA, SERS, cryogenic TEM (cryo-TEM) and circular dichroism (CD) spectroscopy. The tests demonstrated that the protein adsorption on the particles’ surfaces was different for spheroidal and star shaped particles. In our experiments, star shaped particles limited the protein corona formation at SERS “hot spots”. This benefits the small-molecule sensing of nanostars in biological media. This work adds more understanding about protein corona formation on gold nanoparticles of different shapes in biological media, and therefore guides design of particles for studies in vitro and in vivo

Shape dependent protein‐induced stabilization of gold nanoparticles: From a protein corona perspective

Abstract Abstract Gold nanoparticles (AuNPs) are promising materials for many bioapplications. However, upon contacting with biological media, AuNPs undergo changes. The interaction with proteins results in the so‐called protein corona (PC) around AuNPs, leading to the new bioidentity and optical properties. Understanding the mechanisms of PC formation and its functions can help us to utilise its benefits and avoid its drawbacks. To date, most of the previous works aimed to understand the mechanisms governing PC formation and focused on the spherical nanoparticles, although non‐spherical nanoparticles are designed for a wide range of applications in biosensing. In this work, we investigated the differences in PC formation on spherical and anisotropic AuNPs (nanostars in particular) from the joint experimental (extinction spectroscopy, zeta potential and surface‐enhanced Raman scattering [SERS]) and computational methods (the finite element method and molecular dynamics [MD] simulations). We discovered that protein does not fully cover the surface of anisotropic nanoparticles, leaving SERS hot‐spots at the tips and high curvature edges ‘available’ for analyte binding (no SERS signal after pre‐incubation with protein) while providing protein‐induced stabilization (indicated by extinction spectroscopy) of the AuNPs by providing a protein layer around the particle's core. The findings are confirmed from our MD simulations, the adsorption energy significantly decreases with the increased radius of curvature, so that tips (adsorption energy: 2762.334 kJ/mol) would be the least preferential binding site compared to core (adsorption energy: 11819.263 kJ/mol). These observations will help the development of new nanostructures with improved sensing and targeting ability