Interferences of Silica Nanoparticles in Green Fluorescent Protein Folding Processes

Algal extracellular polymeric substance compositions drive the binding characteristics, affinity, and phytotoxicity of graphene oxide in water

Graphene oxide (GO, a popular 2D nanomaterial) poses great potential in water treatment arousing considerable attention regarding its fate and risk in aquatic environments. Extracellular polymeric substances (EPS) exist widely in water and play critical roles in biogeochemical processes. However, the influences of complex EPS fractions on the fate and risk of GO remain unknown in water. This study integrates fluorescence excitation-emission matrix-parallel factor, two-dimensional correlation spectroscopy, and biolayer interferometry studies on the binding characteristics and affinity between EPS fractions and GO. The results revealed the preferential binding of fluorescent aromatic protein-like component, fulvic-like component, and non-fluorescent polysaccharide in soluble EPS (S-EPS) and bound EPS (B-EPS) on GO via π-π stacking and electrostatic interaction that contributed to a higher adsorption capacity of S-EPS on GO and weaker affinity than of B-EPS. Moreover, the EPS fractions drive the morphological and structural alterations, and the attenuated colloid stability of GO in water. Notably, GO-EPS induced stronger phytotoxicity (e.g., photosynthetic damage, and membrane lipid remodeling) compared to pristine GO. Metabolic and functional lipid analysis further elucidated the regulation of amino acid, carbohydrate, and lipid metabolism contributed to the persistent phytotoxicity. This work provides insights into the roles and mechanisms of EPS fractions composition in regulating the environmental fate and risk of GO in natural water.

A double-emission molecularly imprinted ratiometric fluorescent sensor based on carbon quantum dots and fluorescein isothiocyanate for visual detection of p-nitroaniline

A novel molecularly imprinted ratiometric fluorescent sensor CQDs@MIP/FITC@SiO2 for the detection of p-nitroaniline (p-NA) was constructed through the mixture of CQDs@MIP and FITC@SiO2 in the ratio of 1:1 (VCQDs@MIP:VFITC@SiO₂). The polymers of CQDs@MIP and FITC@SiO2 were prepared by sol-gel method and reversed-phase microemulsion method, respectively. CQDs@MIP was used as the auxiliary response signal and FITC@SiO2 was used as the reference enhancement signal. The signal was measured at excitation/emission wavelengths of 365/438, 512 nm. The sensor showed good linearity in the concentration range 0.14-40.00 µM (R2 = 0.998) with a detection limit of 0.042 µM for p-NA. The color change of "blue-cyan-green" could be observed by the naked eye under 365 nm UV light, thus realizing the visual detection of p-NA. The sensor presented comparable results compared with high-performance liquid chromatography (HPLC) method for the detection of p-NA in hair dye paste and aqueous samples with recoveries of 96.8-103.7% and 95.8-104.4%, respectively. It was demonstrated that the constructed sensor possesses the advantages of simplicity, excellent selectivity, superior sensitivity, and outstanding stability.

Expanding Mn2+ loading capacity of BSA via mild non-thermal denaturing and cross-linking as a tool to maximize the relaxivity of water protons

Development of nanoparticles (NPs) serving as contrast enhancing agents in MRI requires a combination of high contrasting effect with the biosafety and hemocompatibility. This work demonstrates that bovine serum albumin (BSA) molecules bound to paramagnetic Mn2+ ions are promising building blocks of such NPs. The desolvation-induced denaturation of BSA bound with Mn2+ ions followed by the glutaraldehyde-facilitated cross-linking provides the uniform in size 102.0 ± 0.7 nm BSA-based nanoparticles (BSA-NPs) loaded with Mn2+ ions, which are manifested in aqueous solutions as negatively charged spheres with high colloid stability. The optimal loading of Mn2+ ions into BSA-NPs provides maximum values of longitudinal and transverse relaxivity at 98.9 and 133.6 mM-1 s-1, respectively, which are among the best known from the literature. The spin trap EPR method indicates that Mn2+ ions bound to BSA-NPs exhibit poor catalytic activity in the Fenton-like reaction. On the contrary, the presence of BSA-NPs has an antioxidant effect by preventing the accumulation of hydroxyl radicals produced by H2O2. The NPs exhibit remarkably low hemolytic activity and hemagglutination can be avoided at concentrations lower than 110 μM. Thus, BSA-NPs bound with Mn2+ ions are promising candidates for combining high contrast effect with biosafety and hemocompatibility.

A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation

Protein aggregation in biotherapeutics can reduce their activity and effectiveness. It may also promote immune reactions responsible for severe adverse effects. The impact of plastic materials on protein destabilization is not totally understood. Here, we propose to deconvolve the effects of material surface, air/liquid interface, and agitation to decipher their respective role in protein destabilization and aggregation. We analyzed the effect of polypropylene, TEFLON, glass and LOBIND surfaces on the stability of purified proteins (bovine serum albumin, hemoglobin and α-synuclein) and on a cell extract composed of 6000 soluble proteins during agitation (P = 0.1-1.2 W/kg). Proteomic analysis revealed that chaperonins, intrinsically disordered proteins and ribosomes were more sensitive to the combined effects of material surfaces and agitation while small metabolic oligomers could be protected in the same conditions. Protein loss observations coupled to Raman microscopy, dynamic light scattering and proteomic allowed us to propose a mechanistic model of protein destabilization by plastics. Our results suggest that protein loss is not primarily due to the nucleation of small aggregates in solution, but to the destabilization of proteins exposed to material surfaces and their subsequent aggregation at the sheared air/liquid interface, an effect that cannot be prevented by using LOBIND tubes. A guidance can be established on how to minimize these adverse effects. Remove one of the components of this combined stress - material, air (even partially), or agitation - and proteins will be preserved.

Competitive protein adsorption on charge regulating silica-like surfaces: the role of protonation equilibrium

We develop a molecular thermodynamic theory to study the interaction of some proteins with a charge regulating silica-like surface under a wide range of conditions, including pH, salt concentration and protein concentration. Proteins are modeled using their three dimensional structure from crystallographic data and the average experimental pKa of amino acid residues. As model systems, we study single-protein and binary solutions of cytochrome c, green fluorescent protein, lysozyme and myoglobin. Our results show that protonation equilibrium plays a critical role in the interactions of proteins with these type of surfaces. The terminal hydroxyl groups on the surface display considerable extent of charge regulation; protein residues with titratable side chains increase protonation according to changes in the local environment and the drop in pH near the surface. This behavior defines protein-surface interactions and leads to the emergence of several phenomena: (i) a complex non-ideal surface charge behavior; (ii) a non-monotonic adsorption of proteins as a function of pH; and (iii) the presence of two spatial regions, a protein-rich and a protein-depleted layer, that occur simultaneously at different distances from the surface when pH is slightly above the isoelectric point of the protein. In binary mixtures, protein adsorption and surface-protein interactions cannot be predicted from single-protein solution considerations.

Engineered Nanoparticle-Protein Interactions Influence Protein Structural Integrity and Biological Significance

Engineered nanoparticles (ENPs) are artificially synthesized particles with unique physicochemical properties. ENPs are being extensively used in several consumer items, elevating the probability of ENP exposure to biological systems. ENPs interact with various biomolecules like lipids, proteins, nucleic acids, where proteins are most susceptible. The ENP-protein interactions are mostly studied for corona formation and its effect on the bio-reactivity of ENPs, however, an in-depth understanding of subsequent interactive effects on proteins, such as alterations in their structure, conformation, free energy, and folding is still required. The present review focuses on ENP-protein interactions and the subsequent effects on protein structure and function followed by the therapeutic potential of ENPs for protein misfolding diseases.

For Whom a Puddle Is the Sea? Adsorption of Organic Guests on Hydrated MCM-41 Silica

Thermal and hydration effects on the mobility of compact and branched organic molecules and a bulky pharmaceutical substance loaded in submonolayer amounts onto mesoporous silica have been elucidated using ¹H and ³¹P solid-state NMR. In all cases, the ambient hydration has a stronger effect than an increase in temperature to 370 K for water-free silica. The effect of hydration depends on the guest and ranges from complete solvation to a silica-water-guest sandwich structure to a silica-guest/silica-water pattern. The mobility of the guests under different conditions has been described. The specific structure of the MCM-41 surface allows one to study very slow surface diffusion, a diffusivity of about 10^-15-10^-16 m²/s. The data reported are relevant to any nonfunctionalized silica, while the method used is applicable to any phosphor-containing guest on any host.

A method to measure the denatured proteins in the corona of nanoparticles based on the specific adsorption of Hsp90ab1

The protein corona influences and determines the biological function of nanoparticles (NPs) in vivo. Analysis and understanding of the activities of proteins in coronas are crucial for nanobiology and nanomedicine research. Misfolded proteins in the corona of NPs theoretically exist, and a protein denaturation-related cellular response might occur in this process as well as in related diseases. The exact evaluation of protein denaturation in the corona is valuable to assess the bioactivities of NPs. Here, we found that the level of adsorbed heat shock protein 90 kDa α class B member 1 (Hsp90ab1) by the denatured protein in iron-cobalt-nickel alloy NPs (FeCoNi NPs) and iron oxide NPs (Fe₃O₄ NPs) was correlated with circular dichroism (CD) analysis and 1-anilinonaphthalene-8-sulfonate (ANS) analysis. The content of Hsp90ab1 in the corona could be easily analysed by western blotting (WB). Further analysis suggested that the method could precisely show the time-dependent protein denaturation on Fe₃O₄ NPs, as well as the influence of the size and the surface modification. More importantly, this method could be applied to other proteins, like lysozyme, other than albumin. Based on the results and the correlation analysis, incubation and detection of Hsp90ab1 in the NP-corona complex can be used as a new and feasible method to evaluate protein denaturation induced by NPs.

In Situ Analysis of Weakly Bound Proteins Reveals Molecular Basis of Soft Corona Formation

Few experimental techniques allow the analysis of the protein corona in situ. As a result, little is known on the effects of nanoparticles on weakly bound proteins that form the soft corona. Despite its biological importance, our understanding of the molecular bases driving its formation is limited. Here, we show that hemoglobin can form either a hard or a soft corona on silica nanoparticles depending on the pH conditions. Using cryoTEM and synchrotron-radiation circular dichroism, we show that nanoparticles alter the structure and the stability of weakly bound proteins in situ. Molecular dynamics simulation identified the structural elements driving protein-nanoparticle interaction. Based on thermodynamic analysis, we show that nanoparticles stabilize partially unfolded protein conformations by enthalpy-driven molecular interactions. We suggest that nanoparticles alter weakly bound proteins by shifting the equilibrium toward the unfolded states at physiological temperature. We show that the classical approach based on nanoparticle separation from the biological medium fails to detect destabilization of weakly bound proteins, and therefore cannot be used to fully predict the biological effects of nanomaterials in situ.

From Protein Corona to Colloidal Self-Assembly: The Importance of Protein Size in Protein-Nanoparticle Interactions

Protein adsorption on nanoparticles is an important field of study, particularly with regard to nanomedicine and nanotoxicology. Many factors can influence the composition and structure of the layer(s) of adsorbed proteins, the so-called protein corona. However, the role of protein size has not been specifically investigated, although some evidence has indicated its potential important role in corona composition and structure. To assess the role of protein size, we studied the interactions of hemoproteins (spanning a large size range) with monodisperse silica nanoparticles. We combined various techniques-adsorption isotherms, isothermal titration calorimetry, circular dichroism, and transmission electron cryomicroscopy-to address this issue. Overall, the results show that small proteins behaved as typical model proteins, forming homogeneous monolayers on the nanoparticle surface (protein corona). Their adsorption is purely enthalpy-driven, with subtle structural changes. In contrast, large proteins interact with nanoparticles via entropy-driven mechanisms. Their structure is completely preserved during adsorption, and any given protein can directly bind to several nanoparticles, forming bridges in these newly formed protein-nanoparticle assemblies. Protein size is clearly an overlooked factor that should be integrated into proteomics and toxicological studies.

Toxicity to RAW264.7 Macrophages of Silica Nanoparticles and the E551 Food Additive, in Combination with Genotoxic Agents

Synthetic amorphous silica (SAS) is used in a plethora of applications and included in many daily products to which humans are exposed via inhalation, ingestion, or skin contact. This poses the question of their potential toxicity, particularly towards macrophages, which show specific sensitivity to this material. SAS represents an ideal candidate for the adsorption of environmental contaminants due to its large surface area and could consequently modulate their toxicity. In this study, we assessed the toxicity towards macrophages and intestinal epithelial cells of three SAS particles, either isolated SiO₂ nanoparticles (LS30) or SiO₂ particles composed of agglomerated-aggregates of fused primary particles, either food-grade (E551) or non-food-grade (Fumed silica). These particles were applied to cells either alone or in combination with genotoxic co-contaminants, i.e., benzo[a]pyrene (B[a]P) and methane methylsulfonate (MMS). We show that macrophages are much more sensitive to these toxic agents than a non-differenciated co-culture of Caco-2 and HT29-MTX cells, used here as a model of intestinal epithelium. Co-exposure to SiO₂ and MMS causes DNA damage in a synergistic way, which is not explained by the modulation of DNA repair protein mRNA expression. Together, this suggests that SiO₂ particles could adsorb genotoxic agents on their surface and, consequently, increase their DNA damaging potential.

Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size does not Matter

Biomolecules, and particularly proteins, bind on nanoparticle (NP) surfaces to form the so-called protein corona. It is accepted that the corona drives the biological distribution and toxicity of NPs. Here, the corona composition and structure were studied using silica nanoparticles (SiNPs) of different sizes interacting with soluble yeast protein extracts. Adsorption isotherms showed that the amount of adsorbed proteins varied greatly upon NP size with large NPs having more adsorbed proteins per surface unit. The protein corona composition was studied using a large-scale label-free proteomic approach, combined with statistical and regression analyses. Most of the proteins adsorbed on the NPs were the same, regardless of the size of the NPs. To go beyond, the protein physicochemical parameters relevant for the adsorption were studied: electrostatic interactions and disordered regions are the main driving forces for the adsorption on SiNPs but polypeptide sequence length seems to be an important factor as well. This article demonstrates that curvature effects exhibited using model proteins are not determining factors for the corona composition on SiNPs, when dealing with complex biological media.

Albumin-driven disassembly of lipidic nanoparticles: the specific case of the squalene-adenosine nanodrug

In the field of nanomedicine, nanostructured nanoparticles (NPs) made of self-assembling prodrugs emerged in the recent years with promising properties. In particular, squalene-based drug nanoparticles have already shown their efficiency through in vivo experiments. However, a complete pattern of their stability and interactions in the blood stream is still lacking. In this work we assess the behavior of squalene-adenosine (SQAd) nanoparticles - whose neuroprotective effect has already been demonstrated in murine models - in the presence of fetal bovine serum (FBS) and of bovine serum albumin (BSA), the main protein of blood plasma. Extensive physicochemical characterizations were performed using Small Angle Neutron Scattering (SANS), cryogenic transmission electron microscopy (Cryo-TEM), circular dichroism (CD), steady-state fluorescence spectroscopy (SSFS) and isothermal titration calorimetry (ITC) as well as in silico by means of ensemble docking simulations with human serum albumin (HSA). Significant changes in the colloidal stability of the nanoparticles in the presence of serum albumin were observed. SANS, CD and SSFS analyses demonstrated an interaction between SQAd and BSA, with a partial disassembly of the nanoparticles in the presence of BSA and the formation of a complex between SQAd and BSA. The interaction free energy of SQAd nanoparticles with BSA derived from ITC experiments, is about -8 kcal mol^-1 which is further supported in silico by ensemble docking simulations. Overall, our results show that serum albumin partially disassembles SQAd nanoparticles by extracting individual SQAd monomers from them. As a consequence, the SQAd nanoparticles would act as a circulating reservoir in the blood stream. The approach developed in this study could be extended to other soft organic nanoparticles.

Combustion and friction-derived nanoparticles and industrial-sourced nanoparticles: The culprit of Alzheimer and Parkinson's diseases

Redox-active, strongly magnetic, combustion and friction-derived nanoparticles (CFDNPs) are abundant in particulate matter air pollution. Urban children and young adults with Alzheimer disease Continuum have higher numbers of brain CFDNPs versus clean air controls. CFDNPs surface charge, dynamic magnetic susceptibility, iron content and redox activity contribute to ROS generation, neurovascular unit (NVU), mitochondria, and endoplasmic reticulum (ER) damage, and are catalysts for protein misfolding, aggregation and fibrillation. CFDNPs respond to external magnetic fields and are involved in cell damage by agglomeration/clustering, magnetic rotation and/or hyperthermia. This review focus in the interaction of CFDNPs, nanomedicine and industrial NPs with biological systems and the impact of portals of entry, particle sizes, surface charge, biomolecular corona, biodistribution, mitochondrial dysfunction, cellular toxicity, anterograde and retrograde axonal transport, brain dysfunction and pathology. NPs toxicity information come from researchers synthetizing particles and improving their performance for drug delivery, drug targeting, magnetic resonance imaging and heat mediators for cancer therapy. Critical information includes how these NPs overcome all barriers, the NPs protein corona changes as they cross the NVU and the complexity of NPs interaction with soluble proteins and key organelles. Oxidative, ER and mitochondrial stress, and a faulty complex protein quality control are at the core of Alzheimer and Parkinson's diseases and NPs mechanisms of action and toxicity are strong candidates for early development and progression of both fatal diseases. Nanoparticle exposure regardless of sources carries a high risk for the developing brain homeostasis and ought to be included in the AD and PD research framework.

Gene to diagnostic: Self immobilizing protein for silica microparticle biosensor, modelled with sarcosine oxidase

A rational design approach is proposed for a multifunctional enzyme reagent for point-of-care diagnostics. The biomaterial reduces downstream isolation steps and eliminates immobilization coupling chemicals for integration in a diagnostic platform. Fusion constructs combined the central functional assay protein (e.g. monomeric sarcosine oxidase, mSOx, horseradish peroxidase, HRP), a visualizing protein (e.g. mCherry) and an in-built immobilization peptide (e.g. R5). Monitoring protein expression in E.coli was facilitated by following the increase in mCherry fluorescence, which could be matched to a color card, indicating when good protein expression has occurred. The R5 peptide (SSKKSGSYSGSKGSKRRIL) provided inbuilt affinity for silica and an immobilization capability for a silica based diagnostic, without requiring additional chemical coupling reagents. Silica particles extracted from beach sand were used to collect protein from crude protein extract with 85-95% selective uptake. The silica immobilized R5 proteins were stable for more than 2 months at room temperature. The K_m for the silica-R5₂-mCh-mSOx-R5-6H was 16.5 ± 0.9 mM (compared with 16.5 ± 0.4 mM, 16.3 ± 0.3 mM, and 16.1 ± 0.4 mM for R5₂-mCh-mSOx-R5-6H, mSOx-R5-6H and mSOx-6H respectively in solution). The use of the "silica-enzymes" in sarcosine and peroxide assays was shown, and a design using particle sedimentation through the sample was examined. Using shadowgraphy and particle image velocimetry the particle trajectory through the sample was mapped and an hourglass design with a narrow waist shown to give good control of particle position. The hourglass biosensor was demonstrated for sarcosine assay in the clinically useful range of 2.5-10 μM in both a dynamic and end point measurement regime.

Importance of Post-translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica surfaces

Understanding the mechanisms involved in the interaction of proteins with inorganic surfaces is of major interest for both basic research and practical applications involving nanotechnology. From the list of cellular proteins with the highest affinity for silica nanoparticles, we highlighted the group of proteins containing arginine-glycine-glycine (RGG) motifs. Biochemical experiments confirmed that RGG motifs interact strongly with the silica surfaces. The affinity of these motifs is further increased when the R residue is asymmetrically, but not symmetrically, dimethylated. Molecular dynamics simulations show that the asymmetrical dimethylation generates an electrostatic asymmetry in the guanidinium group of the R residue, orientating and stabilizing it on the silica surface. The RGG motifs (methylated or not) systematically target the siloxide groups on the silica surface through an ionic interaction, immediately strengthened by hydrogen bonds with proximal silanol and siloxane groups. Given that, in vivo, RGG motifs are often asymmetrically dimethylated by specific cellular methylases, our data add support to the idea that this type of methylation is a key mechanism for cells to regulate the interaction of the RGG proteins with their cellular partners.

The species origin of the serum in the culture medium influences the in vitro toxicity of silica nanoparticles to HepG2 cells

The formation of a protein corona around nanoparticles can influence their toxicity, triggering cellular responses that may be totally different from those elicited by pristine nanoparticles. The main objective of this study was to investigate whether the species origin of the serum proteins forming the corona influences the in vitro toxicity assessment of silica nanoparticles. Coronas were preformed around nanoparticles before cell exposures by incubation in fetal bovine (FBS) or human (HS) serum. The compositions of these protein coronas were assessed by nano-LC MS/MS. The effects of these protein-coated nanoparticles on HepG2 cells were monitored using real-time cell impedance technology. The nanoparticle coronas formed in human or fetal bovine serum comprised many homologous proteins. Using human compared with fetal bovine serum, nanoparticle toxicity in HepG2 cells decreased by 4-fold and 1.5-fold, when used at 50 and 10μg/mL, respectively. It is likely that "markers of self" are present in the serum and are recognized by human cell receptors. Preforming a corona with human serum seems to be more appropriate for in vitro toxicity testing of potential nanocarriers using human cells. In vitro cytotoxicity assays must reflect in vivo conditions as closely as possible to provide solid and useful results.

Alumina nanoparticle-assisted enzyme refolding: A versatile methodology for proteins renaturation

We present a high-yield method for the renaturation of negatively charged enzymes. The approach is based on the use of alumina nanoparticles, which after electrostatic interaction with denatured protein molecules, prevent their aggregation and make the process of refolding controllable. The method, demonstrated by the renaturation of several enzymes, is efficient, rapid, employs a minimal amount of reagents and even can be applied to renature mixture of the denatured enzymes.

Impact of nanoparticles on DNA repair processes: current knowledge and working hypotheses

The potential health effects of exposure to nanomaterials (NMs) is currently heavily studied. Among the most often reported impact is DNA damage, also termed genotoxicity. While several reviews relate the DNA damage induced by NMs and the techniques that can be used to prove such effects, the question of impact of NMs on DNA repair processes has never been specifically reviewed. The present review article proposes to fill this gap of knowledge by critically describing the DNA repair processes that could be affected by nanoparticle (NP) exposure, then by reporting the current state of the art on effects of NPs on DNA repair, at the level of protein function, gene induction and post-transcriptional modifications, and taking into account the advantages and limitations of the different experimental approaches. Since little is known about this impact, working hypothesis for the future are then proposed.

RNA-binding proteins are a major target of silica nanoparticles in cell extracts

Upon contact with biological fluids, nanoparticles (NPs) are readily coated by cellular compounds, particularly proteins, which are determining factors for the localization and toxicity of NPs in the organism. Here, we improved a methodological approach to identify proteins that adsorb on silica NPs with high affinity. Using large-scale proteomics and mixtures of soluble proteins prepared either from yeast cells or from alveolar human cells, we observed that proteins with large unstructured region(s) are more prone to bind on silica NPs. These disordered regions provide flexibility to proteins, a property that promotes their adsorption. The statistical analyses also pointed to a marked overrepresentation of RNA-binding proteins (RBPs) and of translation initiation factors among the adsorbed proteins. We propose that silica surfaces, which are mainly composed of Si-O^- and Si-OH groups, mimic ribose-phosphate molecules (rich in -O^- and -OH) and trap the proteins able to interact with ribose-phosphate containing molecules. Finally, using an in vitro assay, we showed that the sequestration of translation initiation factors by silica NPs results in an inhibition of the in vitro translational activity. This result demonstrates that characterizing the protein corona of various NPs would be a relevant approach to predict their potential toxicological effects.