General, high-affinity approach for the synthesis of fluorophore appended protein nanoparticle assemblies

Exploring the Heterogeneity of Nanoparticles in Their Interactions with Plasma Coagulation Factor XII

Tuning the characteristics of nanoparticles (NPs) would be promising in improving their biocompatibilities, regarding biosafety and nanodrug considerations. Due to the high priority of the artificial NPs in contacting the circulatory system, understanding their interactions with plasma zymogens is of great importance. Four kinds of NPs, including 5 nm gold NPs (GNP-5), 5 and 20 nm silver NPs (SNP-5, SNP-20), and 20 nm silica NPs (SiNP-20), were investigated for their interactions with the coagulation factor XII (FXII). GNP-5 adsorbed FXII in a standing-up mode, and exhibited high binding affinity for the heavy chain of the protein without altering its secondary structure or inducing its activation. In contrast to GNP-5, FXII adsorption on the other tested NPs was in a lying-down mode, and their interactions with FXII induced its conformational changes, thus causing the evident zymogen cleavage. The structural alterations and activation of FXII induced by the NPs exhibited in specific surface area dependent manners, which were related with different NP cores and sizes. Additionally, the enzymatic activity of α-FXIIa was also influenced by NP incubation, and the alterations were dependent on the specific characters of the NPs as evidenced by the enzymatic inhibition effect of GNP-5 (noncompetitive) and SNP-5 (competitive), and enhanced enzymatic catalysis abilities of SNP-20 and SiNP-20. The interesting findings on the heterogeneity of NPs in their interactions with plasma FXII not only revealed the underlying mechanism for NP-triggered hematological responses, but also suggested the crucial role of tuning NP parameters in their potential bioapplication, like nanodrug design.

Probing the binding affinity of plasma proteins adsorbed on Au nanoparticles

Nanoparticle (NP) surfaces are modified immediately by the adsorption of proteins when exposed to human blood, leading to the formation of a protein corona. The adsorption of serum proteins is the key process for exploring the bioapplication and biosafety of NPs. In this study, NP-protein binding affinity (K_a) was investigated. Some serum proteins, such as human serum albumin (HSA), trypsin (TRP), hemoglobin (Hb), myoglobin (MB), immunoglobulin G (IgG), carbonic anhydrase (CA), fibrinogen (FIB), chymotrypsin and r-globulin, were used with gold nanoparticles (AuNPs) to address binding affinity according to isothermal titration calorimetry (ITC) combined with dynamic light scattering (DLS) and fluorescence quenching. The NP protein binding affinities determined by the two methods were in agreement, and depended on the protein properties and size of the NPs. The two methods are convenient, and the results are highly comparable. These methods can be extended to determine the binding affinity of NP protein interactions. The adsorption of proteins upon the AuNP surface is a complex process and depends on several factors, but the binding affinities are higher for proteins with more cysteine residues located on the surface.

Effects of surface compositional and structural heterogeneity on nanoparticle-protein interactions: different protein configurations

As nanoparticles (NPs) enter into biological systems, they are immediately exposed to a variety and concentration of proteins. The physicochemical interactions between proteins and NPs are influenced by the surface properties of the NPs. To identify the effects of NP surface heterogeneity, the interactions between bovine serum albumin (BSA) and gold NPs (AuNPs) with similar chemical composition but different surface structures were investigated. Different interaction modes and BSA conformations were studied by dynamic light scattering, circular dichroism spectroscopy, fluorescence quenching and isothermal titration calorimetry (ITC). Depending on the surface structure of AuNPs, BSA seems to adopt either a "side-on" or an "end-on" conformation on AuNPs. ITC demonstrated that the adsorption of BSA onto AuNPs with randomly distributed polar and nonpolar groups was primarily driven by electrostatic interaction, and all BSA were adsorbed in the same process. The adsorption of BSA onto AuNPs covered with alternating domains of polar and nonpolar groups was a combination of different interactions. Overall, the results of this study point to the potential for utilizing nanoscale manipulation of NP surfaces to control the resulting NP-protein interactions.

Wide dynamic range sensing with single quantum dot biosensors

Single-particle analysis of biosensors that use charge transfer as the means for analyte-dependent signaling with semiconductor nanoparticles, or quantum dots, was examined. Single-particle analysis of biosensors that use energy transfer show analyte-dependent switching of nanoparticle emission from off to on. The charge-transfer-based biosensors reported here show constant emission, where the analyte (maltose) increases the emission intensity. By monitoring the same nanoparticles under various conditions, a single charge-transfer-based biosensor construct (one maltose binding protein, one protein attachment position for the reductant, one type of nanoparticle) showed a dynamic range for analyte (maltose) detection spanning from 100 pM to 10 μM while the emission intensities increase from 25 to 175% at the single-particle level. Since these biosensors were immobilized, the correlation between the detected maltose concentration and the maltose-dependent emission intensity increase could be examined. Minimal correlation between maltose detection limits and emission increases was observed, suggesting a variety of reductant-nanoparticle surface interactions that control maltose-dependent emission intensity responses. Despite the heterogeneous responses, monitoring biosensor emission intensity over 5 min provided a quantifiable method to monitor maltose concentration. Immobilizing and tracking these biosensors with heterogeneous responses, however, expanded the analyte-dependent emission intensity and the analyte dynamic range obtained from a single construct. Given the wide dynamic range and constant emission of charge-transfer-based biosensors, applying these single molecule techniques could provide ultrasensitive, real-time detection of small molecules in living cells.

Physicochemical characteristics of protein-NP bioconjugates: the role of particle curvature and solution conditions on human serum albumin conformation and fibrillogenesis inhibition

Gold nanoparticles (Au NPs) from 5 to 100 nm in size synthesized with HAuCl(4) and sodium citrate were complexed with the plasma protein human serum albumin (HSA). Size, surface charge, and surface plasmon bands of the Au NPs are largely modified by the formation of a protein corona via electrostatic interactions and hydrogen bonding as revealed by thermodynamic data. Negative values of the entropy of binding suggested a restriction in the biomolecule mobility upon adsorption. The structure of the adsorbed protein molecules is slightly affected by the interaction with the metal surface, but this effect is enhanced as the NP curvature decreases. Also, it is observed that the protein molecules adsorbed onto the NP surface are more resistant to complete thermal denaturation than free protein ones as deduced from the increases in the melting temperature of the adsorbed protein. Differences in the conformations of the adsorbed protein molecules onto small (<40 nm) and large NPs were observed on the basis of ζ-potential data and FTIR spectroscopy, also suggesting a better resistance of adsorbed protein molecules to thermal denaturing conditions. We think this enhanced protein stability is responsible for a reduced formation of HSA amyloid-like fibrils in the presence of small Au NPs under HSA fibrillation conditions.

The controlled display of biomolecules on nanoparticles: a challenge suited to bioorthogonal chemistry

Interest in developing diverse nanoparticle (NP)-biological composite materials continues to grow almost unabated. This is motivated primarily by the desire to simultaneously exploit the properties of both NP and biological components in new hybrid devices or materials that can be applied in areas ranging from energy harvesting and nanoscale electronics to biomedical diagnostics. The utility and effectiveness of these composites will be predicated on the ability to assemble these structures with control over NP/biomolecule ratio, biomolecular orientation, biomolecular activity, and the separation distance within the NP-bioconjugate architecture. This degree of control will be especially critical in creating theranostic NP-bioconjugates that, as a single vector, are capable of multiple functions in vivo, including targeting, image contrast, biosensing, and drug delivery. In this review, a perspective is given on current and developing chemistries that can provide improved control in the preparation of NP-bioconjugates. The nanoscale properties intrinsic to several prominent NP materials are briefly described to highlight the motivation behind their use. NP materials of interest include quantum dots, carbon nanotubes, viral capsids, liposomes, and NPs composed of gold, lanthanides, silica, polymers, or magnetic materials. This review includes a critical discussion on the design considerations for NP-bioconjugates and the unique challenges associated with chemistry at the biological-nanoscale interface-the liabilities of traditional bioconjugation chemistries being particularly prominent therein. Select bioorthogonal chemistries that can address these challenges are reviewed in detail, and include chemoselective ligations (e.g., hydrazone and Staudinger ligation), cycloaddition reactions in click chemistry (e.g., azide-alkyne cyclyoaddition, tetrazine ligation), metal-affinity coordination (e.g., polyhistidine), enzyme driven modifications (e.g., HaloTag, biotin ligase), and other site-specific chemistries. The benefits and liabilities of particular chemistries are discussed by highlighting relevant NP-bioconjugation examples from the literature. Potential chemistries that have not yet been applied to NPs are also discussed, and an outlook on future developments in this field is given.

Binding of ReO4(-) with an engineered MoO4(2-)-binding protein: towards a new approach in radiopharmaceutical applications

Radiolabeled biomolecules are routinely used for clinical diagnostics. (99m)Tc is the most commonly used radioactive tracer in radiopharmaceuticals. (188)Re and (186)Re are also commonly used as radioactive tracers in medicine. However, currently available methods for radiolabeling are lengthy and involve several steps in bioconjugation processes. In this work we present a strategy to engineer proteins that may selectively recognize the perrhenate (ReO(4)(-)) ion as a new way to label proteins. We found that a molybdate (MoO(4)(2-))-binding protein (ModA) from Escherichia coli can bind perrhenate with high affinity. Using fluorescence and isothermal titration calorimetry measurements, we determined the dissociation constant of ModA for ReO(4)(-) to be 541 nM and we solved a crystal structure of ModA with a bound ReO(4)(-). On the basis of the structure we created a mutant protein containing a disulfide linkage, which exhibited increased affinity for perrhenate (K(d) = 104 nM). High-resolution crystal structures of ModA (1.7 Å) and A11C/R153C mutant (2.0 Å) were solved with bound perrhenate. Both structures show that a perrhenate ion occupies the molybdate binding site using the same amino acid residues that are involved in molybdate binding. The overall structure of the perrhenate-bound ModA is unchanged compared with that of the molybdate-bound form. In the mutant protein, the bound perrhenate is further stabilized by the engineered disulfide bond.

Geometry and surface characteristics of gold nanoparticles influence their biodistribution and uptake by macrophages

Spherical and rod-shaped gold nanoparticles with surface poly(ethylene glycol) (PEG) chains were characterized for size, shape, charge, poly dispersity and surface plasmon resonance. The nanoparticles were injected intravenously to 6-8-week-old female nu/nu mice bearing orthotopic ovarian tumors, and their biodistribution in vital organs was compared. Gold nanorods were taken up to a lesser extent by the liver, had longer circulation time in the blood, and higher accumulation in the tumors, compared with their spherical counterparts. The cellular uptake of PEGylated gold nanoparticles by a murine macrophage-like cell line as a function of geometry was examined. Compared to nanospheres, PEGylated gold nanorods were taken up to a lesser extent by macrophages. These studies point to the importance of gold nanoparticle geometry and surface properties on transport across biological barriers.

Simultaneous detection of attomolar pathogen DNAs by Bio-MassCode mass spectrometry

A general method is described to analyze pathogen DNAs in homogenous solution by a novel Bio-MassCode probe, using a small organic (namely disulfide) "reporter mass" that self-assembled in oligonucleotide-modified gold nanoparticles. With conventional MALDI TOF MS, the assay simultaneously detected DNAs for HIV, HBV, HCV, and TP with extraordinarily high sensitivity in the low attomolar (10(-18) M) range without any other amplification.

Interaction of gold nanoparticles with common human blood proteins

In order to better understand the physical basis of the biological activity of nanoparticles (NPs) in nanomedicine applications and under conditions of environmental exposure, we performed an array of photophysical measurements to quantify the interaction of model gold NPs having a wide range of NP diameters with common blood proteins. In particular, absorbance, fluorescence quenching, circular dichroism, dynamic light scattering, and electron microscopy measurements were performed on surface-functionalized water-soluble gold NPs having a diameter range from 5 to 100 nm in the presence of common human blood proteins: albumin, fibrinogen, gamma-globulin, histone, and insulin. We find that the gold NPs strongly associate with these essential blood proteins where the binding constant, K, as well as the degree of cooperativity of particle--protein binding (Hill constant, n), depends on particle size and the native protein structure. We also find tentative evidence that the model proteins undergo conformational change upon association with the NPs and that the thickness of the adsorbed protein layer (bare NP diameter <50 nm) progressively increases with NP size, effects that have potential general importance for understanding NP aggregation in biological media and the interaction of NP with biological materials broadly.

Protein design provides lead(II) ion biosensors for imaging molecular fluxes around red blood cells

Metalloprotein design and semiconductor nanoparticles have been combined to generate a reagent for selective fluorescence imaging of Pb(2+) ions in the presence red blood cells. A biosensor system based on semiconductor nanoparticles provides the photonic properties for small molecule measurement in and around red blood cells. Metalloprotein design was used to generate a Pb(2+) ion selective receptor from a protein that is structurally homologous to a protein used previously in this biosensing system. Parameters for the Pb(2+) ion binding site were derived from crystallographic structures of low molecular weight Pb(2+) ion complexes that contain a stereoactive lone pair. When the designed protein was produced and attached to ZnS-coated CdSe nanoparticles, two Pb(NO(3))(2)-associated binding events were observed (2-fold emission decrease; K(A1) = 1 x 10(9) M(-1); K(A2) = 3.5 x 10(6) M(-1)). The fluorescence response had a 100 pM Pb(NO(3))(2) detection limit, while no response was observed with Ca(2+) ions (10 mM), Zn(2+) ions (100 muM), or Cd(2+) ions (100 muM). Metal ion selectivity presumably comes from the coordination geometry selected to favor lone pair formation on Pb(2+) ions and electrostatically disfavor tetrahedral coordination. Replacement of ZnS-coated CdSe with ZnS-coated InGaP nanoparticles provided similar biosensors (100 pM limit of detection; K(A1) = 1 x 10(9) M(-1); K(A2) = 1 x 10(7) M(-1)) but with excitation/emission wavelengths longer than the major absorbance of red blood cell hemoglobin (>620 nm). The InGaP nanoparticle-based biosensors provided a 5 nM Pb(NO(3))(2) detection limit in the presence of red blood cells. The modularity of the biosensor system provides exchangeable Pb(2+) ion detection around red blood cells.

Unimolecular, soluble semiconductor nanoparticle-based biosensors for thrombin using charge/electron transfer

Duplex DNA was attached to semiconductor nanoparticles providing selective detection of thrombin. Using the method reported here, semiconductor nanoparticles can have selective sensory functions for a host of additional analytes in the future. The system uses one DNA strand that selectively binds an analyte (thrombin), while the complementary DNA strand contains a redox-active metal complex. The accessibility of the metal complex to the nanoparticle surface is increased upon thrombin binding due to unravelling of the duplex DNA secondary structure. Increased interactions between the metal complex and the nanoparticle surface will decrease nanoparticle emission intensity, through charge transfer. Initially, water-soluble nanoparticles with carboxylate-terminated monolayers showed thrombin-specific responses in emission intensity (-30% for 1:1 nanoparticle to DNA, +50% for 1:5). Despite the selective responses, the thrombin binding isotherms indicated multiple binding equilibria and more than likely nanoparticle aggregation. The need for a nonaggregative system comes from the potential employment of these sensors in live cell or living system fluorescence assays. By changing the nanoparticle capping ligand to provide an ethylene glycol-terminated monolayer, the binding isotherms fit a two-state binding model with a thrombin dissociation constant of 3 nM in a physiologically relevant buffer. This article demonstrates the need to consider capping ligand effects in designing biosensors based on semiconductor nanoparticles and demonstrates an initial DNA-attached semiconductor nanoparticle system that uses DNA-analyte binding interactions (aptamers).

Controlled nanoparticleassembly through protein conformational changes

Selective surface recognition by proteins provides programmed bottom-up assembly of synthetic nanomaterials. We have investigated the controlled self-assembly of functionalized gold nanoparticles (Au-TAsp) with cytochrome c (Cyt c) and apoCyt c through complementary electrostatic interactions. Au-TAsp formed discrete, water-soluble adducts with native Cyt c, whereas unfolded apoCyt c induced nanocomposite formation at high Cyt c : Au-TAsp ratios. The binding of random-coil apoCyt c to Au-TAsp at low ratios induced α-helix formation in soluble nanocomposites, but at elevated ratios insoluble micron-scale aggregates were formed. The local structure of the assemblies was critically dependent on the Cyt c : Au-TAsp ratio. The dispersibility of apoCyt c-Au-TAsp was pH dependent, providing rapid and reversible control over nanocomposite assembly. The apoCyt c-Au-TAsp aggregates could likewise be disassembled through proteolytic cleavage of apoCyt c, demonstrating the ability to selectively remodel these hybrid materials.

Quantum dots and peptides: a bright future together

Nanocrystalline semi-conductor materials, called quantum dots (QDs), exhibit unique optical and spectroscopic properties, which include, broad absorption, narrow and tunable emission, resistance to photobleaching, strong luminescence, and long luminescent lifetimes. These remarkable properties of QDs have resulted in their use as an alternative to both small-molecule and protein fluorophores in innumerable biological applications. The overlap of QDs with the rich chemistry and biology that is characteristic of the peptide arena is an emerging research area. Peptides engineered with appropriate cysteines or histidines have served as ligands for producing water soluble QDs as well as for tagging protein ligands and biosensors to QD surfaces. Incorporation of cell-penetrating peptides on QD surfaces has allowed for the translocation of functionalized QDs into cells for intracellular imaging applications. QDs containing fluorescently labeled peptide substrates have shown utility in the development of novel protease assays. Moreover, QDs-labeled peptides that serve as ligands for cellular receptors provide an alternative to antibody mediated imaging at the whole-cell and single molecule level to study receptor distribution and trafficking. This review highlights the overlap between QD and peptide chemistry and speculates on future research directions.

Proteolytic activity monitored by fluorescence resonance energy transfer through quantum-dot-peptide conjugates

Proteases are enzymes that catalyse the breaking of specific peptide bonds in proteins and polypeptides. They are heavily involved in many normal biological processes as well as in diseases, including cancer, stroke and infection. In fact, proteolytic activity is sometimes used as a marker for some cancer types. Here we present luminescent quantum dot (QD) bioconjugates designed to detect proteolytic activity by fluorescence resonance energy transfer. To achieve this, we developed a modular peptide structure which allowed us to attach dye-labelled substrates for the proteases caspase-1, thrombin, collagenase and chymotrypsin to the QD surface. The fluorescence resonance energy transfer efficiency within these nanoassemblies is easily controlled, and proteolytic assays were carried out under both excess enzyme and excess substrate conditions. These assays provide quantitative data including enzymatic velocity, Michaelis-Menten kinetic parameters, and mechanisms of enzymatic inhibition. We also screened a number of inhibitory compounds against the QD-thrombin conjugate. This technology is not limited to sensing proteases, but may be amenable to monitoring other enzymatic modifications.

Selective, reversible, reagentless maltose biosensing with core–shell semiconducting nanoparticles

Reagentless and reversible maltose biosensors are demonstrated using ZnS coated CdSe (CdSe@ZnS) nanoparticle emission intensities. This method is based on electron transfer quenching of unimolecular protein-CdSe@ZnS nanoparticle assemblies, which is provided by a protein-attached Ru(II) complex. This Ru(II) complex is presumed to reduce a valence band hole of the CdSe@ZnS excited state by tunneling through the ZnS overcoating. The Ru(II) complex mediated quenching of CdSe@ZnS nanoparticle emission was only decreased 1.2-fold relative to the CdSe nanoparticle systems. While four different Ru(II) complex attachment sites provided different amounts of nanoparticle emission quenching (1.20 to 1.75-fold decrease), all of these attachment sites yielded maltose-dependent intensity changes (1.1 to 1.4-fold increase upon maltose addition). Maltose dissociation constants for these four biosensing systems range from 250 nM to 1.0 microM, which are similar to the maltose-maltose binding protein dissociation constant that these sensors are based on. The increased fluorescence intensity was found to only occur in the presence of maltose. Furthermore, the ability of these reagentless protein-nanoparticle assemblies to perform maltose biosensing reversibly is demonstrated with the addition of alpha-glucosidase. Three 50 microM maltose additions after alpha-glucosidase addition showed increases of 2.2 microM, 600 nM, and 150 nM maltose. This result demonstrates a fluorometric method for examining alpha-glucosidase activity. Using maltose binding protein to control Ru(II) complex interactions with CdSe@ZnS nanoparticle surfaces provide a novel class of highly fluorescent, photostable biosensors that are selective for maltose.