Dynamic Light-Scattering Analysis of the Electrostatic Interaction of Hexahistidine-Tagged Cytochrome P450 Enzyme with Semiconductor Quantum Dots

Binding-Mediated Formation of Ribonucleoprotein Corona for Efficient Delivery and Control of CRISPR/Cas9

Protein coronae formed with nanoparticles confer several useful properties. However, the non-specific nature of protein corona formation makes it difficult to deliver specific proteins for therapeutic applications. Herein, we report on the construction of a new type of protein corona, termed binding-mediated protein corona. This new corona enables the efficient and controllable delivery of functional proteins, which is otherwise challenging for conventional protein coronae. We show the design and delivery of the ribonucleoprotein corona for the CRISPR/Cas9 system. Successful gene editing in human cell lines (Hela and HEK293) demonstrates the efficient delivery, high stability, low cytotoxicity, and well-controlled activity of the Cas9-guide RNA ribonucleoprotein. The binding-mediated protein corona strategy opens up new opportunities for therapeutic protein delivery.

Protein-nanoparticle interactions and a new insight

The study of protein-nanoparticle interactions provides knowledge about the bio-reactivity of nanoparticles, and creates a database of nanoparticles for applications in nanomedicine, nanodiagnosis, and nanotherapy. The problem arises when nanoparticles come in contact with physiological fluids such as plasma or serum, wherein they interact with the proteins (or other biomolecules). This interaction leads to the coating of proteins on the nanoparticle surface, mostly due to the electrostatic interaction, called 'corona'. These proteins are usually partially unfolded. The protein corona can deter nanoparticles from their targeted functionalities, such as drug/DNA delivery at the site and fluorescence tagging of diseased tissues. The protein corona also has many repercussions on cellular intake, inflammation, accumulation, degradation, and clearance of the nanoparticles from the body depending on the exposed part of the proteins. Hence, the protein-nanoparticle interaction and the configuration of the bound-proteins on the nanosurface need thorough investigation and understanding. Several techniques such as DLS and zeta potential measurement, UV-vis spectroscopy, fluorescence spectroscopy, circular dichroism, FTIR, and DSC provide valuable information in the protein-nanoparticle interaction study. Besides, theoretical simulations also provide additional understanding. Despite a lot of research publications, the fundamental question remained unresolved. Can we aim for the application of functional nanoparticles in medicine? A new insight, given by us, in this article assumes a reasonable solution to this crucial question.

In Vivo Retargeting of Poly(beta aminoester) (OM-PBAE) Nanoparticles is Influenced by Protein Corona

One of the main bottlenecks in the translation of nanomedicines from research to clinics is the difficulty in designing nanoparticles actively vectorized to the target tissue, a key parameter to ensure efficacy and safety. In this group, a library of poly(beta aminoester) polymers is developed, and it is demonstrated that adding specific combinations of terminal oligopeptides (OM-PBAE), in vitro transfection is cell selective. The current study aims to actively direct the nanoparticles to the liver by the addition of a targeting molecule. To achieve this objective, retinol, successfully attached to OM-PBAE, is selected as hepatic targeting moiety. It is demonstrated that organ biodistribution is tailored, achieving the desired liver accumulation. Regarding cell type transfection, antigen presenting cells in the liver are those showing the highest transfection. Thanks to proteomics studies, organ but not cellular biodistribution can be explained by the formation of differential protein coronas. Therefore, organ biodistribution is governed by differential protein corona formed when retinol is present, while cellular biodistribution is controlled by the end oligopeptides type. In summary, this work is a proof of concept that demonstrates the versatility of these OM-PBAE nanoparticles, in terms of the modification of the biodistribution of OM-PBAE nanoparticles adding active targeting moieties.

Enzyme Adsorption on Nanoparticle Surface Probed by Highly Sensitive Second Harmonic Light Scattering

Recent developments in second harmonic light scattering technique and the associated theoretical models have provided a deeper insight of molecular interactions on micro- and nanoparticle surfaces. This technique is extended to probe the thermodynamics of protein adsorption on nanoparticle surface which is crucial for understanding the fate of nanoparticle-based formulations in biomedical applications. A modified Langmuir adsorption model has been applied to extract the thermodynamic parameters from the experimental data. The general applicability of the technique is established by extracting free energy change, association constant, and binding stoichiometry of adsorption of a moderate size protein, alcohol dehydrogenase, and a small size protein, insulin, on gold nanoparticles. The free energy change for the adsorption is found to be of the order of -55kJ/mol, which indicates that the interaction of proteins with the nanoparticle surface involves weak forces. On the other hand, the low value of the free energy change makes the detachment of the protein from the particle surface easier and guarantees reversibility of the binding process. In addition, one gets the binding stoichiometry of the proteins with the nanoparticle surface which opens up the possibility of controlling the payload of the protein- or peptide-based therapeutics in future biomedical applications.

Nanospherical arabinogalactan proteins are a key component of the high-strength adhesive secreted by English ivy

Over 130 y have passed since Charles Darwin first discovered that the adventitious roots of English ivy (Hedera helix) exude a yellowish mucilage that promotes the capacity of this plant to climb vertical surfaces. Unfortunately, little progress has been made in elucidating the adhesion mechanisms underlying this high-strength adhesive. In the previous studies, spherical nanoparticles were observed in the viscous exudate. Here we show that these nanoparticles are predominantly composed of arabinogalactan proteins (AGPs), a superfamily of hydroxyproline-rich glycoproteins present in the extracellular spaces of plant cells. The spheroidal shape of the AGP-rich ivy nanoparticles results in a low viscosity of the ivy adhesive, and thus a favorable wetting behavior on the surface of substrates. Meanwhile, calcium-driven electrostatic interactions among carboxyl groups of the AGPs and the pectic acids give rise to the cross-linking of the exuded adhesive substances, favor subsequent curing (hardening) via formation of an adhesive film, and eventually promote the generation of mechanical interlocking between the adventitious roots of English ivy and the surface of substrates. Inspired by these molecular events, a reconstructed ivy-mimetic adhesive composite was developed by integrating purified AGP-rich ivy nanoparticles with pectic polysaccharides and calcium ions. Information gained from the subsequent tensile tests, in turn, substantiated the proposed adhesion mechanisms underlying the ivy-derived adhesive. Given that AGPs and pectic polysaccharides are also observed in bioadhesives exuded by other climbing plants, the adhesion mechanisms revealed by English ivy may forward the progress toward understanding the general principles underlying diverse botanic adhesives.

Gold Nanoparticles Decorated with Sialic Acid Terminated Bi-antennary N-Glycans for the Detection of Influenza Virus at Nanomolar Concentrations

Gold nanoparticles decorated with full-length sialic acid terminated complex bi-antennary N-glycans, synthesized with glycans isolated from egg yolk, were used as a sensor for the detection of both recombinant hemagglutinin (HA) and whole influenza A virus particles of the H1N1 subtype. Nanoparticle aggregation was induced by interaction between the sialic acid termini of the glycans attached to gold and the multivalent sialic acid binding sites of HA. Both dynamic light scattering (DLS) and UV/Vis spectroscopy demonstrated the efficiency of the sensor, which could detect viral HA at nanomolar concentrations and revealed a linear relationship between the extent of nanoparticle aggregation and the concentration of HA. UV/Vis studies also showed that these nanoparticles can selectively detect an influenza A virus strain that preferentially binds sialic acid terminated glycans with α(2→6) linkages over a strain that prefers glycans with terminal α(2→3)-linked sialic acids.

Analysis of quantum dots and their conjugates by capillary electrophoresis with detection of laser-induced luminescence

In many bioanalytical applications, important molecules such as DNA, proteins, and antibodies are routinely conjugated with fluorescent tags to reach an extraordinary sensitivity of analyses. Semiconductor nanoparticles, quantum dots, have already proved to be suitable components of highly luminescent tags, probes, and sensors with a broad applicability in analytical chemistry. Quantum dots provide high extinction coefficients together with a wide range of excitation wavelengths, size- and composition-tunable emissions, narrow and symmetric emission spectra, good quantum yields, relatively long size-dependent luminescence lifetime, and practically no photobleaching. Most of these properties are superior when compared with conventional organic fluorescent dyes. In this chapter, optimized procedures for the preparation of water-dispersed cadmium telluride (CdTe) quantum dots, conjugating reactions with antibodies, DNA, and macrocycles as well as their analyses by capillary electrophoresis are described. The potential of capillary electrophoresis for fast analyses of nanoparticles, their conjugates with antibodies, and immunocomplexes with targeted antigens is demonstrated on examples.

The Role of PEG Conformation in Mixed Layers: From Protein Corona Substrate to Steric Stabilization Avoiding Protein Adsorption

<p>Although nanoparticles have been traditionally modified with a single ligand layer, mixture of ligands might help to combine different functionalities and to further engineer the NP surface. A detailed study of the competition between an alkanethiol (11-mercaptoundecanoic acid) and SH-PEG for the surface of AuNPs and the resultant behaviors of this model nanoconjugate is presented here. As a result, the physicochemical properties of these conjugates can be progressively tuned by controlling the composition and especially the conformation of the mixed monolayer. This has implications in the physiological stability. The controlled changes on the SH-PEG conformation rather than its concentration induces a change in the stabilization mechanism from electrostatic repulsion to steric hindrance, which changes the biological fate of NPs. Importantly, the adsorption of proteins on the conjugates can be tailored by tuning the composition and conformation of the mixed layer.</p>

Mechanistic basis of electron transfer to cytochromes p450 by natural redox partners and artificial donor constructs

Cytochromes P450 (P450s) are hemoproteins catalyzing oxidative biotransformation of a vast array of natural and xenobiotic compounds. Reducing equivalents required for dioxygen cleavage and substrate hydroxylation originate from different redox partners including diflavin reductases, flavodoxins, ferredoxins and phthalate dioxygenase reductase (PDR)-type proteins. Accordingly, circumstantial analysis of structural and physicochemical features governing donor-acceptor recognition and electron transfer poses an intriguing challenge. Thus, conformational flexibility reflected by togging between closed and open states of solvent exposed patches on the redox components was shown to be instrumental to steered electron transmission. Here, the membrane-interactive tails of the P450 enzymes and donor proteins were recognized to be crucial to proper orientation toward each other of surface sites on the redox modules steering functional coupling. Also, mobile electron shuttling may come into play. While charge-pairing mechanisms are of primary importance in attraction and complexation of the redox partners, hydrophobic and van der Waals cohesion forces play a minor role in docking events. Due to catalytic plasticity of P450 enzymes, there is considerable promise in biotechnological applications. Here, deeper insight into the mechanistic basis of the redox machinery will permit optimization of redox processes via directed evolution and DNA shuffling. Thus, creation of hybrid systems by fusion of the modified heme domain of P450s with proteinaceous electron carriers helps obviate the tedious reconstitution procedure and induces novel activities. Also, P450-based amperometric biosensors may open new vistas in pharmaceutical and clinical implementation and environmental monitoring.

The nanoparticle biomolecule corona: lessons learned – challenge accepted?

Besides the wide use of engineered nanomaterials (NMs) in technical products, their applications are not only increasing in biotechnology and biomedicine, but also in the environmental field.

Enzyme nanoarchitectonics: organization and device application

Fabrication of ultrasmall functional machines and their integration within ultrasmall areas or volumes can be useful for creation of novel technologies. The ultimate goal of the development of ultrasmall machines and device systems is to construct functional structures where independent molecules operate as independent device components. To realize exotic functions, use of enzymes in device structures is an attractive solution because enzymes can be regarded as efficient machines possessing high reaction efficiencies and specificities and can operate even under ambient conditions. In this review, recent developments in enzyme immobilization for advanced functions including device applications are summarized from the viewpoint of micro/nano-level structural control, or nanoarchitectonics. Examples are roughly classified as organic soft matter, inorganic soft materials or integrated/organized media. Soft matter such as polymers and their hybrids provide a medium appropriate for entrapment and encapsulation of enzymes. In addition, self-immobilization based on self-assembly and array formation results in enzyme nanoarchitectures with soft functions. For the confinement of enzymes in nanospaces, hard inorganic mesoporous materials containing well-defined channels play an important role. Enzymes that are confined exhibit improved stability and controllable arrangement, which are useful for formation of functional relays and for their integration into artificial devices. Layer-by-layer assemblies as well as organized lipid assemblies such as Langmuir-Blodgett films are some of the best media for architecting controllable enzyme arrangements. The ultrathin forms of these films facilitate their connection with external devices such as electrodes and transistors. Artificial enzymes and enzyme-mimicking catalysts are finally briefly described as examples of enzyme functions involving non-biological materials. These systems may compensate for the drawbacks of natural enzymes, such as their instabilities under harsh conditions. We believe that enzymes and their mimics will be freely coupled, organized and integrated upon demand in near future technologies.

Cytochrome P450 enzyme functionalized-quantum dots as photocatalysts for drug metabolism

A light-controlled drug metabolism system was successfully designed by using cytochrome P450 2C9 (CYP2C9) functionalized CdTe QDs as photocatalysts.

A facile method for the detection of DNA by using gold nanoparticle probes coupled with dynamic light scattering

In this paper, we present a simple and rapid method for deoxyribonucleic acid (DNA) detection using gold nanoparticle probes coupled with dynamic light scattering (DLS) analysis. The redox agent 1,4-dithio-dl-threitol cross-links the gold nanoparticles (AuNPs) to form clusters, while the monothiol DNA could terminate the formation and stabilize the assembled clusters by their negatively charge-based repulsions. By varying the concentration of DNA, the different sizes of DNA-AuNP clusters can be obtained. The sizes of the DNA-AuNP clusters were determined by DLS. A linear correlation was obtained between the sizes and the logarithm of DNA concentration from 2 nM to 5 μM with a detection limit of 1 nM (S/N = 3).

Rational nanoconjugation improves biocatalytic performance of enzymes: aldol addition catalyzed by immobilized rhamnulose-1-phosphate aldolase

Gold nanoparticles (AuNPs) are attractive materials for the immobilization of enzymes due to several advantages such as high enzyme loading, absence of internal diffusion limitations, and Brownian motion in solution, compared to the conventional immobilization onto porous macroscopic supports. The affinity of AuNPs to different groups present at the protein surface enables direct enzyme binding to the nanoparticle without the need of any coupling agent. Enzyme activity and stability appear to be improved when the biocatalyst is immobilized onto AuNPs. Rhamnulose-1-phosphate aldolase (RhuA) was selected as model enzyme for the immobilization onto AuNPs. The enzyme loading was characterized by four different techniques: surface plasmon resonance (SPR) shift and intensity, dynamic light scattering (DLS), and transmission electron microscopy (TEM). AuNPs-RhuA complexes were further applied as biocatalyst of the aldol addition reaction between dihydroxyacetone phosphate (DHAP) and (S)-Cbz-alaninal during two reaction cycles. In these conditions, an improved reaction yield and selectivity, together with a fourfold activity enhancement were observed, as compared to soluble RhuA.

Interaction of Water-Soluble CdTe Quantum Dots with Bovine Serum Albumin

Semiconductor nanoparticles (quantum dots) are promising fluorescent markers, but it is very little known about interaction of quantum dots with biological molecules. In this study, interaction of CdTe quantum dots coated with thioglycolic acid (TGA) with bovine serum albumin was investigated. Steady state spectroscopy, atomic force microscopy, electron microscopy and dynamic light scattering methods were used. It was explored how bovine serum albumin affects stability and spectral properties of quantum dots in aqueous media. CdTe-TGA quantum dots in aqueous solution appeared to be not stable and precipitated. Interaction with bovine serum albumin significantly enhanced stability and photoluminescence quantum yield of quantum dots and prevented quantum dots from aggregating.

Lead (II) ion detection in surface water with pM sensitivity using aza-crown-ether-modified silver nanoparticles via dynamic light scattering

In this paper, we reported ultrasensitive lead ion detection in environmental water with pM sensitivity using aza-crown-ether-modified silver nanoparticles (ACE-Ag NPs) through dynamic light scattering (DLS). The colorimetric method based on ACE-Ag NPs is not capable of detecting Pb2+ ions over other metal ions (Fe3+, Co2+, Cu2+, Hg2+, Cd2+, Ag+, Li+, Na+, K+ and Cs+) with high sensitivity. But DLS has improved the selectivity and sensitivity of the Pb2+ detection system (50-fold or more) over colorimetric method, and its detection limit is 0.25 pM (1.03 ppt). The Pb2+ DLS assay can be applied to detect Pb2+ in the environmental water, such as in Yangtze and East Lake water samples with a detection limit of 0.20 and 0.22 pM, which is much lower than the maximum contamination level of 4.8×10(-8) M for lead in surface water defined by the national environmental quality standards of China (GB 3838-2002). Also, this method has a good performance in the determination of Pb2+ in drinking water, which is much lower than the maximum contamination level (MCL) of 72 nM for lead as defined by the US Environmental Protection Agency (EPA).

Capillary electrophoresis immunoassays with conjugated quantum dots

Water-soluble CdTe quantum dots (QDs) and their conjugates with antibodies and antigenes were prepared by optimized procedures for applications in CE immunoassays. The QD size of 3.5 nm, excitation spectrum in the range of 300-500 nm, the maximum wavelength of the emission spectrum at 610 nm, quantum yield of 0.25 and luminescence lifetimes in the range of 3.6-43 ns were determined. The 0.1 M solution of TRIS/TAPS (pH 8.3) was found to be the optimum buffer for the separation of the antiovalbumin-ovalbumin immunocomplex from the free conjugates of QDs.

Highly sensitive and selective dynamic light-scattering assay for TNT detection using p-ATP attached gold nanoparticle

TNT is one of the most commonly used nitro aromatic explosives for landmines of military and terrorist activities. As a result, there is an urgent need for rapid and reliable methods for the detection of trace amount of TNT for screenings in airport, analysis of forensic samples, and environmental analysis. Driven by the need to detect trace amounts of TNT from environmental samples, this article demonstrates a label-free, highly selective, and ultrasensitive para-aminothiophenol (p-ATP) modified gold nanoparticle based dynamic light scattering (DLS) probe for TNT recognition in 100 pico molar (pM) level from ethanol:acetonitile mixture solution. Because of the formation of strong π-donor-acceptor interaction between TNT and p-ATP, para-aminothiophenol attached gold nanoparticles undergo aggregation in the presence of TNT, which changes the DLS intensity tremendously. A detailed mechanism for significant DLS intensity change has been discussed. Our experimental results show that TNT can be detected quickly and accurately without any dye tagging in 100 pM level with excellent discrimination against other nitro compounds.

Analytical strategies for detecting nanoparticle-protein interactions

A significant increase in biomedical applications of nanomaterials and their potential toxicity demands versatile analytical techniques to determine protein-nanoparticle (NP) interactions. These diverse analytical techniques are reviewed. Spectroscopic methods play a significant role in studying binding affinity, binding ratio, and binding mechanisms. To elucidate NP-proteome interactions, chromatography and electrophoresis techniques are applied to separate NP-bound proteins and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to identify these proteins. Since NP-protein binding is a dynamic event, surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) are methods of choice to study the kinetics of NP-protein binding.

Screening for cytochrome p450 reactivity by harnessing catalase as reporter enzyme

Cytochrome P450 enzymes are known to catalyze a variety of reactions that are difficult to perform by standard organic synthesis, such as the oxidation of unactivated C--C bonds. Cytochrome P450 enzymes can also be used in artificial systems in which organic peroxides act as cosubstrates. To find substrates that are converted by a certain P450 catalyst in the presence of an organic peroxide, various screening assays have been established, however, most of them are limited to one or only a few specific substrates. Here, we report a simple and rapid screening assay that works independently of the nature of the substrate and utilizes a previously undescribed reactivity of catalase as reporter enzyme. In an initial demonstration of this assay, we screened 180 enzyme/peroxide/substrate combinations for potential bioconversions. As shown by subsequent verification of the screening results with liquid chromatography/multistage mass spectrometry (LC/MS(n)), we were able to identify three new substrates for the enzyme CYP152A1 and at least two previously undescribed conversions by the enzyme CYP119.

Live cell labeling of glial progenitor cells using targeted quantum dots

This study describes the development of targeted quantum dots (T-QDs) as biomarkers for the labeling of glial progenitor cells (GPCs) that over express platelet derived growth factor (PDGF) and its receptor PDGFR (GPC(PDGF)). PDGFR plays a critical role in glioma development and growth, and is also known to affect multiple biological processes such as cell migration and embryonic development. T-QDs were developed using streptavidin-conjugated quantum dots (S-QDs) with biotinylated antibodies and utilized to label the intracellular and extracellular domains of live, cultured GPC(PDGF) cells via lipofection with cationic liposomes. Confocal studies illustrate successful intracellular and extracellular targeted labeling within live cells that does not appear to impact upstream PDGFR dynamics during real-time signaling events. Further, T-QDs were nontoxic to GPC(PDGF) cells, and did not alter cell viability or proliferation over the course of 6 days. These results raise new applications for T-QDs as ultra sensitive agents for imaging and tracking of protein populations within live cells, which that will enable future mechanistic study of oncogenic signaling events in real-time.

Intracellular delivery of quantum dot-protein cargos mediated by cell penetrating peptides

We utilize cell penetrating peptide functionalized QDs as specific vectors for the intracellular delivery of model fluorescent protein cargos. Multiple copies of two structurally diverse fluorescent proteins, the 27 kDa monomeric yellow fluorescent protein and the 240 kDa multichromophore b-phycoerythrin complex, were attached to QDs using either metal-affinity driven self-assembly or biotin-Streptavidin binding, respectively. Cellular uptake of these complexes was found to depend on the additional presence of cell-penetrating peptides within the QD-protein conjugates. Once inside the cells, the QD conjugates were mostly distributed within endolysosomal compartments, indicating that intracellular delivery of both QD assemblies was primarily driven by endocytotic uptake. Cellular microinjection of QD-fluorescent protein assemblies was also utilized as an alternate delivery strategy that could bypass the endocytic pathway. Simultaneous signals from both the QDs and the fluorescent proteins allowed verification of their colocalization and conjugate integrity upon delivery inside live cells. Due to their intrinsic fluorescence properties, this class of proteins provides a unique tool to test the ability of QDs functionalized with cell penetrating peptides to mediate the intracellular delivery of both small and large size protein cargos. Use of QD-peptide/fluorescent protein vectors may make powerful tools for understanding the mechanisms of nanoparticle-mediated drug delivery.

Quantum dot fluorescence quenching pathways with Cr(III) complexes. photosensitized NO production from trans-Cr(cyclam)(ONO)2+

Described is the photoluminescence (PL) of water-soluble CdSe/ZnS core/shell quantum dots (QDs) as perturbed by salts of the chromium(III) complexes trans-Cr(cyclam)Cl2+ (1), trans-Cr(cyclam)(ONO)2+ (2), and trans-Cr(cyclam)(CN)2+ (3) (cyclam = 1,4,8,11-tetraazacyclo-tetradecane). The purpose is to probe the characteristics of such QDs as antennae for photosensitized release of bioactive agents (in the present case, the bioregulatory molecule NO) from transition metal centers. Addition of 1 or 2 to a QD solution results in concentration-dependent quenching of the band edge emission, but 3 has a minimal effect. Added KCl strongly attenuates the quenching by 1, and this suggests that the Cr(III) cations and the QDs form electrostatic assemblies via ion pairing on the negatively charged QD surfaces. Quenching by 2, a known photochemical NO precursor, was accompanied by photosensitized NO release. All three, however, do quench the broad red emission ( approximately 650-850 nm) attributed to radiative decay of surface trapped carriers. The effect of various concentrations of 1 on time-resolved PL and absorbance were explored using ultrafast spectroscopic methods. These observations are interpreted in terms of the Förster resonance energy-transfer mechanism for quenching of the band edge PL by multiple units of 1 or 2 at the QD surface, whereas quenching of the low-energy trap emission occurs via a charge-transfer pathway.