Binding kinetics of ultrasmall gold nanoparticles with proteins

Realizing active targeting in cancer nanomedicine with ultrasmall nanoparticles

Ultrasmall nanoparticles (usNPs) have emerged as promising theranostic tools in cancer nanomedicine. With sizes comparable to globular proteins, usNPs exhibit unique physicochemical properties and physiological behavior distinct from larger particles, including lack of protein corona formation, efficient renal clearance, and reduced recognition and sequestration by the reticuloendothelial system. In cancer treatment, usNPs demonstrate favorable tumor penetration and intratumoral diffusion. Active targeting strategies, incorporating ligands for specific tumor receptor binding, serve to further enhance usNP tumor selectivity and therapeutic performance. Numerous preclinical studies have already demonstrated the potential of actively targeted usNPs, revealing increased tumor accumulation and retention compared to non-targeted counterparts. In this review, we explore actively targeted inorganic usNPs, highlighting their biological properties and behavior, along with applications in both preclinical and clinical settings.

Biomolecular Corona of Gold Nanoparticles: The Urgent Need for Strong Roots to Grow Strong Branches

Gold nanoparticles (GNPs) are largely employed in diagnostics/biosensors and are among the most investigated nanomaterials in biology/medicine. However, few GNP-based nanoformulations have received FDA approval to date, and promising in vitro studies have failed to translate to in vivo efficacy. One key factor is that biological fluids contain high concentrations of proteins, lipids, sugars, and metabolites, which can adsorb/interact with the GNP's surface, forming a layer called biomolecular corona (BMC). The BMC can mask prepared functionalities and target moieties, creating new surface chemistry and determining GNPs' biological fate. Here, the current knowledge is summarized on GNP-BMCs, analyzing the factors driving these interactions and the biological consequences. A partial fingerprint of GNP-BMC analyzing common patterns of composition in the literature is extrapolated. However, a red flag is also risen concerning the current lack of data availability and regulated form of knowledge on BMC. Nanomedicine is still in its infancy, and relying on recently developed analytical and informatic tools offers an unprecedented opportunity to make a leap forward. However, a restart through robust shared protocols and data sharing is necessary to obtain "stronger roots". This will create a path to exploiting BMC for human benefit, promoting the clinical translation of biomedical nanotools.

Functionalized GD2 Electrochemical Immunosensor to Diagnose Minimum Residual Disease of Bone Marrow in Neuroblastoma Effectively

Neuroblastoma (NB) is known as the "king of childhood tumors" due to its highly metastatic, recurrence-prone, and difficult-to-treat characteristics. International Neuroblastoma Risk Grading Group (INRG) has recommended GD2, a disialoganglioside expressed on neuroectodermal tumor cells, as the target for detecting minimal residual disease in bone marrow metastases of high-risk neuroblastoma in children. Therefore, accurately identifying GD2-positive cells is crucial for diagnosing children with high-risk NB. Here, we designed a graphene/AuNP/GD2 Ab-functionalized electrochemical biosensor for GD2 detection. A three-electrode system was processed using a screen-printed technique with a working electrode of indium tin oxide, a counter electrode of carbon, and a reference electrode of silver/silver chloride. Graphene/AuNPs were modified on the indium tin oxide electrode using chronoamperometric scans, and then, the GD2 antibody was modified on the biosensor by electrostatic adsorption to achieve sensitive and specific detection of GD2-positive cells in bone marrow fluid. The results showed that a graphene/AuNP/GD2 Ab-functionalized electrochemical biosensor achieved GD2-positive cell detection in the range of 102 cells/mL~105 cells/mL by differential pulse voltammetry. Bone marrow fluid samples from 12 children with high-risk NB were retained for testing on our biosensor and showed 100% compliance with the clinical application of the gold-standard immunocytochemical staining technique for detecting GD2-positive cells qualitatively. The GD2-based electrochemical assay can accurately detect children with high-risk NB, providing a rapidly quantitative basis for clinical diagnosis and treatment.

Time Evolution of Ultrasmall Gold Nanoparticle-Protein Interactions

To date, much effort has been devoted toward the study of protein corona formation onto large gold nanoparticles (GNPs). However, the protein corona concept breaks down for GNPs in the ultrasmall size regime (<3 nm), and, as a result, our understanding of ultrasmall GNP (usGNP)-protein interactions remains incomplete. Herein, we used anionic usGNPs and six different proteins as model systems to systematically investigate usGNP-protein interactions, with particular focus on the time evolution and long-term behavior of complex formation. The different proteins comprised chymotrypsin (Cht), trypsin (Try), thrombin (Thr), serum albumin (HSA), cytochrome c (Cyt c), and factor XII (FXII). We used a range of biochemical and biophysical methods to estimate binding affinities, determine the effects of usGNPs on protein structure and function, assess the reversibility of any protein structural and functional changes, and evaluate usGNP-protein complex stability. Among the main findings, we observed that prolonged (24 h)─but not short-term (10 min)─interactions between proteins and usGNPs permanently altered protein function, including enzyme activities (Try, Thr, and FXIIa), peroxidase-like activity (Cyt c), and ligand-binding properties (HSA). Remarkably, this occurred without any large-scale loss of the native global conformation, implying time-dependent effects of usGNPs on local protein conformation or dynamics. We also found that both short-(10 min) and long-term (24 h) interactions between proteins and usGNPs yielded short-lived complexes, i.e., there was no time-dependent "hardening" of the interactions at the binding interface as usually seen with large GNPs. The present study increases our fundamental understanding of nano-bio interactions in the ultrasmall size regime, which may assist the safe and effective translation of usGNPs into the clinic.

Aptamer-conjugated gold nanoparticles and their diagnostic and therapeutic roles in cancer

The burden of incidence rate and mortality of cancer is increasing rapidly, and the development of precise intervention measures for cancer detection and treatment will help reduce the burden and pain of cancer. At present, the sensitivity and specificity of tumor markers such as CEA and CA-125 used clinically are low, while PET, SPECT, and other imaging diagnoses with high sensitivity possess shortcomings, including long durations to obtain formal reports and the inability to identify the molecular pathological type of cancer. Cancer surgery is limited by stage and easy to recur. Radiotherapy and chemotherapy often cause damage to normal tissues, leading to evident side effects. Aptamers can selectively and exclusively bind to biomarkers and have, therefore, gained attention as ligands to be targeted for cancer detection and treatment. Gold nanoparticles (AuNPs) are considered as promising nano carriers for cancer diagnosis and treatment due to their strong light scattering characteristics, effective biocompatibility, and easy surface modification with targeted agents. The aptamer-gold nanoparticles targeting delivery system developed herein can combine the advantages of aptamers and gold nanoparticles, and shows excellent targeting, high specificity, low immunogenicity, minor side effects, etc., which builds a bridge for cancer markers to be used in early and efficient diagnosis and precise treatment. In this review, we summarize the latest progress in the application of aptamer-modified gold nanoparticles in cancer targeted diagnosis and delivery of therapeutic agents to cancer cells and emphasize the prospects and challenges of transforming these studies into clinical applications.

New Paradigm for Nano-Bio Interactions: Multimolecular Assembly of a Prototypical Disordered Protein with Ultrasmall Nanoparticles

Understanding the interactions between nanoparticles (NPs) and proteins is crucial for the successful application of NPs in biological contexts. Protein adsorption is dependent on particle size, and protein binding to ultrasmall (1-3 nm) NPs is considered to be generally weak. However, most studies have involved structured biomacromolecules, while the interactions of ultrasmall NPs with intrinsically disordered proteins (IDPs) have remained elusive. IDPs are abundant in eukaryotes and found to associate with NPs intracellularly. As a model system, we focused on ultrasmall gold nanoparticles (usGNPs) and tau, a cytosolic IDP associated with Alzheimer's disease. Using site-resolved NMR, steady-state fluorescence, calorimetry, and circular dichroism, we reveal that tau and usGNPs form stable multimolecular assemblies, representing a new type of nano-bio interaction. Specifically, the observed interaction hot spots explain the influence of usGNPs on tau conformational transitions, with implications for the intracellular targeting of aberrant IDP aggregation.

Anionic Ultrasmall Gold Nanoparticles Bind to Coagulation Factors and Disturb Normal Hemostatic Balance

Ultrasmall gold nanoparticles (usNPs) and nanoclusters are an emerging class of nanomaterials exhibiting distinctive physicochemical properties and in vivo behaviors. Although understanding the interactions of usNPs with blood components is of fundamental importance to advance their clinical translation, currently, little is known about the way that usNPs interact with the hemostatic system. This study describes the effects of a model anionic p-mercaptobenzoic acid-coated usNP on the coagulation cascade, with particular emphasis on the contact pathway. It is found that in a purified system, the anionic usNPs bind to and activate factor XII (FXII). The formed usNP-FXII complexes are short-lived (residence time of ∼10 s) and characterized by an affinity constant of ∼200 nM. In human plasma, the anionic usNPs activate the contact pathway and promote coagulation. The usNPs also exhibit anticoagulant activity in plasma by interfering with the thrombin-mediated cleavage of fibrinogen. Taken together, these findings establish that anionic usNPs can disturb the normal hemostatic balance, which in turn may hinder their clinical translation. Finally, it is shown that usNPs can be designed to be nearly inert in plasma by surface coating with the natural peptide glutathione.

CeO2-Zn Nanocomposite Induced Superoxide, Autophagy and a Non-Apoptotic Mode of Cell Death in Human Umbilical-Vein-Derived Endothelial (HUVE) Cells

In this study, a nanocomposite of cerium oxide-zinc (CeO₂-Zn; 26 ± 11 nm) based on the antioxidant rare-earth cerium oxide (CeO₂) nanoparticles (NPs) with the modifier zinc (Zn) was synthesized by sintering method and characterized. Its bio-response was examined in human umbilical-vein-derived endothelial (HUVE) cells to get insight into the components of vascular system. While NPs of CeO₂ did not significantly alter cell viability up to a concentration of 200 µg/mL for a 24 h exposure, 154 ± 6 µg/mL of nanocomposite CeO₂-Zn induced 50% cytotoxicity. Mechanism of cytotoxicity occurring due to nanocomposite by its Zn content was compared by choosing NPs of ZnO, possibly the closest nanoparticulate form of Zn. ZnO NPs lead to the induction of higher reactive oxygen species (ROS) (DCF-fluorescence), steeper depletion in antioxidant glutathione (GSH) and a greater loss of mitochondrial membrane potential (MMP) as compared to that induced by CeO₂-Zn nanocomposite. Nanocomposite of CeO₂-Zn, on the other hand, lead to significant higher induction of superoxide radical (O₂^•−, DHE fluorescence), nitric oxide (NO, determined by DAR-2 imaging and Griess reagent) and autophagic vesicles (determined by Lysotracker and monodansylcadeverine probes) as compared to that caused by ZnO NP treatment. Moreover, analysis after triple staining (by annexin V-FITC, PI, and Hoechst) conducted at their respective IC50s revealed an apoptosis mode of cell death due to ZnO NPs, whereas CeO₂-Zn nanocomposite induced a mechanism of cell death that was significantly different from apoptosis. Our findings on advanced biomarkers such as autophagy and mode of cell death suggested the CeO₂-Zn nanocomposite might behave as independent nanostructure from its constituent ones. Since nanocomposites can behave independently of their constituent NPs/elements, by creating nanocomposites, NP versatility can be increased manifold by just manipulating existing NPs. Moreover, data in this study can furnish early mechanistic insight about the potential damage that could occur in the integrity of vascular systems.

Scratching the Surface of the Protein Corona: Challenging Measurements and Controversies

This Review aims to provide a systematic analysis of the literature regarding ongoing debates in protein corona research. Our goal is to portray the current understanding of two fundamental and debated characteristics of the protein corona, namely, the formation of mono- or multilayers of proteins and their binding (ir)reversibility. The statistical analysis we perform reveals that these characterisitics are strongly correlated to some physicochemical factors of the NP-protein system (particle size, bulk material, protein type), whereas the technique of investigation or the type of measurement (in situ or ex situ) do not impact the results, unlike commonly assumed. Regarding the binding reversibility, the experimental design (either dilution or competition experiments) is also shown to be a key factor, probably due to nontrivial protein binding mechanisms, which could explain the paradoxical phenomena reported in the literature. Overall, we suggest that to truly predict and control the protein corona, future efforts should be directed toward the mechanistic aspects of protein adsorption.

Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing

Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP–GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold–sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry.

Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

The use of nanoparticles (NPs) in biomedicine has made a gradual transition from proof-of-concept to clinical applications, with several NP types meeting regulatory approval or undergoing clinical trials. A new type of metallic nanostructures called ultrasmall nanoparticles (usNPs) and nanoclusters (NCs), while retaining essential properties of the larger (classical) NPs, have features common to bioactive proteins. This combination expands the potential use of usNPs and NCs to areas of diagnosis and therapy traditionally reserved for small-molecule medicine. Their distinctive physicochemical properties can lead to unique in vivo behaviors, including improved renal clearance and tumor distribution. Both the beneficial and potentially deleterious outcomes (cytotoxicity, inflammation) can, in principle, be controlled through a judicious choice of the nanocore shape and size, as well as the chemical ligands attached to the surface. At present, the ability to control the behavior of usNPs is limited, partly because advances are still needed in nanoengineering and chemical synthesis to manufacture and characterize ultrasmall nanostructures and partly because our understanding of their interactions in biological environments is incomplete. This review addresses the second limitation. We review experimental and computational methods currently available to understand molecular mechanisms, with particular attention to usNP-protein complexation, and highlight areas where further progress is needed. We discuss approaches that we find most promising to provide relevant molecular-level insight for designing usNPs with specific behaviors and pave the way to translational applications.

Artificial neural networks for the inverse design of nanoparticles with preferential nano-bio behaviors

Safe and efficient use of ultrasmall nanoparticles (NPs) in biomedicine requires numerous independent conditions to be met, including colloidal stability, selectivity for proteins and membranes, binding specificity, and low affinity for plasma proteins. The ability of a NP to satisfy one or more of these requirements depends on its physicochemical characteristics, such as size, shape, and surface chemistry. Multiscale and pattern recognition techniques are here integrated to guide the design of NPs with preferential nano-bio behaviors. Data systematically collected from simulations (or experiments, if available) are first used to train one or more artificial neural networks, each optimized for a specific kind of nano-bio interaction; the trained networks are then interconnected in suitable arrays to obtain the NP core morphology and layer composition that best satisfy all the nano-bio interactions underlying more complex behaviors. This reverse engineering approach is illustrated in the case of NP-membrane interactions, using binding modes and affinities and early stage membrane penetrations as training data. Adaptations for designing NPs with preferential nano-protein interactions and for optimizing solution conditions in the test tube are discussed.

Adsorption of proteins on oral Zn2+ doped iron oxide nanoparticles in mouse stomach and in vitro: triggering nanoparticle aggregation

Oral route is one of the most important portals of nanoparticle entry to the body. However, in vivo protein corona formed in the gastrointestinal tract has not been studied owing to the difficulty for the recovery of nanoparticles from the in vivo environment. In this study, by using the magnetic property of iron oxide nanoparticles (Fe3O4 NPs) and Zn2+ doped iron oxide nanoparticles (Zn0.4Fe2.6O4 NPs), the nanoparticles were separated from the gastric fluid after oral administration in mice. The effects of Zn2+ doping and static magnetic field (SMF) treatment on the protein adsorption on the nanoparticles were investigated in vitro and in vivo. Zn2+ doping decreases the adsorption of pepsin on the nanoparticles in vitro and affects the composition of the protein corona in vivo and enhances protein adsorption-induced aggregation of the nanoparticles in vitro and in vivo. SMF treatment affects the composition of the protein corona of Fe3O4 NPs and Zn0.4Fe2.6O4 NPs, and enhances the aggregation of Fe3O4 NPs and Zn0.4Fe2.6O4 NPs in vivo. Furthermore, the results demonstrate that electrostatic attraction is the crucial force to drive adsorption of proteins on Fe3O4 NPs and Zn0.4Fe2.6O4 NPs and protein adsorption-induced change in the surface charge of nanoparticles plays an important role in the pH-dependent aggregation of the nanoparticles. In addition, the work provides the evidence that the protein adsorption-induced aggregation of Fe3O4 NPs and Zn0.4Fe2.6O4 NPs has no effect on their magnetic susceptibility. The results highlight that Zn0.4Fe2.6O4 NPs may be used as a potential oral magnetic resonance imaging contrast agent in diagnosis of gastrointestinal disease.

Quantitative mechanistic model for ultrasmall nanoparticle-protein interactions

To date, extensive effort has been devoted toward the characterization of protein interactions with synthetic nanostructures. However, much remains to be understood, particularly concerning microscopic mechanisms of interactions. Here, we have conducted a detailed investigation of the kinetics of nanoparticle-protein complexation to gain deeper insights into the elementary steps and molecular events along the pathway for complex formation. Toward that end, the binding kinetics between p-mercaptobenzoic acid-coated ultrasmall gold nanoparticles (AuMBA) and fluorescently-labeled ubiquitin was investigated at millisecond time resolution using stopped-flow spectroscopy. It was found that both the association and dissociation kinetics consisted of multiple exponential phases, hence suggesting a complex, multi-step reaction mechanism. The results fit into a picture where complexation proceeds through the formation of a weakly-bound first-encounter complex with an apparent binding affinity (KD) of ∼9 μM. Encounter complex formation is followed by unimolecular tightening steps of partial desolvation/ion removal and conformational rearrangement, which, collectively, achieve an almost 100-fold increase in affinity of the final bound state (apparent KD ∼0.1 μM). The final state is found to be weakly stabilized, displaying an average lifetime in the range of seconds. Screening of the electrostatic forces at high ionic strength weakens the AuMBA-ubiquitin interactions by destabilizing the encounter complex, whereas the average lifetime of the final bound state remains largely unchanged. Overall, our rapid kinetics investigation has revealed novel quantitative insights into the molecular-level mechanisms of ultrasmall nanoparticle-protein interactions.

Regulation of Thrombin Activity with Ultrasmall Nanoparticles: Effects of Surface Chemistry

Nanomaterials displaying well-tailored sizes and surface chemistries can provide novel ways with which to modulate the structure and function of enzymes. Recently, we showed that gold nanoparticles (AuNPs) in the ultrasmall size regime could perform as allosteric effectors inducing partial inhibition of thrombin activity. We now find that the nature of the AuNP surface chemistry controls the interactions to the anion-binding exosites 1 and 2 on the surface of thrombin, the allosterically induced changes to the active-site conformation, and, by extension, the enzymatic activity. Ultrasmall AuNPs passivated with p-mercaptobenzoic acid ligands (AuMBA) and a peptide-based (Ac-ECYN) biomimetic coat (AuECYN) were utilized in our investigations. Remarkably, we found that while AuMBA binds to exosites 1 and 2, AuECYN interacts primarily with exosite 2. It was further established that AuMBA behaves as a "mild denaturant" of thrombin leading to catalytic dysfunction over time. Conversely, AuECYN resembles a proper allosteric effector leading to partial and reversible inhibition of the activity. Collectively, our findings reveal how the distinct binding modes of different AuNP types may uniquely influence thrombin structure and catalysis. The present study further contributes to our understanding of how synthetic nanomaterials could be exploited in the allosteric regulation of enzymes.

Ultrasmall Gold Nanoparticles Coated with Zwitterionic Glutathione Monoethyl Ester: A Model Platform for the Incorporation of Functional Peptides

Ultrasmall gold nanoparticles (AuNPs) are an emerging class of nanomaterials exhibiting distinctive physicochemical, molecular, and in vivo properties. Recently, we showed that ultrasmall AuNPs encompassing a zwitterionic glutathione monoethyl ester surface coating (AuGSHzwt) were highly resistant to aggregation and serum protein interactions. Herein, we performed a new set of biointeraction studies to gain a more fundamental understanding into the behavior of both pristine and peptide-functionalized AuGSHzwt in complex media. Using the model Strep-tag peptide (WSHPQFEK) as an integrated functional group, we established that AuGSHzwt could be conjugated with increasing numbers of Strep-tags by simple ligand exchange, which provides a generic approach for AuGSHzwt functionalization. It was found that the strep-tagged AuGSHzwt particles were highly resistant to nonspecific protein interactions and retained their targeting capability in biological fluid, displaying efficient binding to Streptactin receptors in nearly undiluted serum. However, AuGSHzwt functionalized with multiple Strep-tags displayed somewhat lower resistance to protein interactions and lower levels of binding to Streptactin than monofunctionalized AuGSHzwt under given conditions. These results underscore the need for optimizing ligand density onto the surface of ultrasmall AuNPs for improved performance. Collectively, our findings support ultrasmall AuGSHzwt as an attractive platform for engineering functional, protein-mimetic nanostructures capable of specific protein recognition within the complex biological milieu.

High Surface Reactivity and Biocompatibility of Y2O3 NPs in Human MCF-7 Epithelial and HT-1080 FibroBlast Cells

This study aimed to generate a comparative data on biological response of yttrium oxide nanoparticles (Y₂O₃ NPs) with the antioxidant CeO₂ NPs and pro-oxidant ZnO NPs. Sizes of Y₂O₃ NPs were found to be in the range of 35±10 nm as measured by TEM and were larger from its hydrodynamic sizes in water (1004 ± 134 nm), PBS (3373 ± 249 nm), serum free culture media (1735 ± 305 nm) and complete culture media (542 ± 108 nm). Surface reactivity of Y₂O₃ NPs with bovine serum albumin (BSA) was found significantly higher than for CeO₂ and ZnO NPs. The displacement studies clearly suggested that adsorption to either BSA, filtered serum or serum free media was quite stable, and was dependent on whichever component interacted first with the Y₂O₃ NPs. Enzyme mimetic activity, like that of CeO₂ NPs, was not detected for the NPs of Y₂O₃ or ZnO. Cell viability measured by MTT and neutral red uptake (NRU) assays suggested Y₂O₃ NPs were not toxic in human breast carcinoma MCF-7 and fibroblast HT-1080 cells up to the concentration of 200 μg/mL for a 24 h treatment period. Oxidative stress markers suggested Y₂O₃ NPs to be tolerably non-oxidative and biocompatible. Moreover, mitochondrial potential determined by JC-1 as well as lysosomal activity determined by lysotracker (LTR) remained un-affected and intact due to Y₂O₃ and CeO₂ NPs whereas, as expected, were significantly induced by ZnO NPs. Hoechst-PI dual staining clearly suggested apoptotic potential of only ZnO NPs. With high surface reactivity and biocompatibility, NPs of Y₂O₃ could be a promising agent in the field of nanomedicine.

A model beyond protein corona: thermodynamics and binding stoichiometries of the interactions between ultrasmall gold nanoclusters and proteins

Nanoparticles (NPs) will inevitably interact with proteins and form protein coronas once they are exposed to biological fluids. This conventional model for nano-bio interactions has been used for over twenty years. Growing numbers of new nanomaterials are emerging every year. Among them, noble metal nanoclusters (NMNCs) are new types of fluorescent nanomaterials with considerable advantages in biomedical applications. Compared with NPs (typically >10 nm) like Au NPs, carbon nanotubes, etc., NMNCs have ultrasmall sizes (∼2 nm), so when NMNCs are exposed to biological milieu, will they form protein coronas like NPs? Due to a lack of characterization techniques for ultrasmall nanoparticles (USNPs), to date, studies on the binding stoichiometries of USNPs to proteins have been heavily hampered. To address this challenge, we combined the characteristics of various methods and selected human serum albumin (HSA) and transferrin (Trf) as model proteins to study their interactions with dihydrolipoic acid (DHLA) protected gold nanoclusters (DHLA-AuNCs). Steady-state fluorescence, transient fluorescence spectroscopy and isothermal titration calorimetry (ITC) were used to study the thermodynamic parameters (K, ΔH, ΔS, ΔG) and interaction mechanisms. The results showed that the intrinsic fluorescence of both proteins was quenched by DHLA-AuNCs, and the quenching process of HSA was an endothermic dynamic process. In contrast, the quenching process of Trf was an exothermic static process. The combination of ITC, agarose gel electrophoresis (AGE) and zeta potential showed that one HSA could bind 8 ± 1 DHLA-AuNCs and one Trf could bind 7 ± 2 DHLA-AuNCs, which was quite different from the conventional model of protein coronas. Based on these findings, the "protein complex" was termed for proteins upon binding with USNPs. Dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) showed that DHLA-AuNCs could induce the agglomeration of proteins. Circular dichroism (CD) and synchronous fluorescence spectroscopy showed that DHLA-AuNCs had a very minor effect on the secondary structures of HSA and Trf, which demonstrated the good biocompatibility of DHLA-AuNCs at the molecular scale. This work has shed light on a new interaction model beyond the protein corona, indicating a possible biological identity of USNPs.

Strong dependence of the nano-bio interactions on core morphology and layer composition of ultrasmall nanostructures

The interactions between nanoparticles (NPs) and proteins, cells, and tissues, broadly known as nano-bio interactions, depend on the NP size and shape and on the characteristics of the NP coating layer, such as density, thickness, and chemical makeup. The dependence of nano-membrane interactions on the design parameters of ultrasmall nanostructures is studied by computer simulations. Considered here are spheres, plates, rings, rods, tubes, and helices made up of either bare magnetite or passivated gold, interacting with charged or zwitterionic membranes. The analysis reveals a strong dependence on shape, size, and layer composition of various quantities that characterize the nano-bio behavior, including binding modes and affinities. This sensitivity can be exploited to design nanostructures that bind preferentially to membranes or that stabilize or disrupt membrane structural integrity. The method used here is general and not limited to the ultrasmall regime, so it can be adopted to study other nano-bio interactions systematically. The implications for the distribution of NPs in cells and tissues (biodistribution) and for passive and active transmembrane transport are discussed, both important processes in biomedicine.

Impact of soft protein interactions on the excretion, extent of receptor occupancy and tumor accumulation of ultrasmall metal nanoparticles: a compartmental model simulation

Ultrasmall metal nanoparticles (NPs) are next-generation nano-based platforms for in vivo disease diagnosis and treatment. Due to their small size below the kidney filtration threshold and marked resistance to nonspecific serum protein adsorption, ultrasmall NPs can be rapidly excreted through the kidneys and escape liver uptake. However, although ultrasmall particles may be deemed highly resistant to protein adsorption, the real extent of this resistance is not known. Here, a simple compartmental model simulation was therefore implemented to understand how NP behavior in vivo could be modulated by soft, transient NP-plasma protein interactions characterized by dissociation constants in the millimolar range. In Model 1, ultrasmall NPs functionalized with a targeting probe, plasma proteins and target receptors were assumed to co-exist within a single compartment. Simulations were performed to understand the synergistic effect of soft interactions, systemic clearance and NP size on receptor occupancy in the single compartment. The results revealed the existence of a narrow range of ultraweak affinities and optimal particle sizes leading to greater target occupancy. In Model 2, simulations were performed to understand the impact of soft interactions on NP accumulation into a peripheral (tumor) compartment. The results revealed that soft interactions - but not active targeting - enhanced tumor uptake levels when tumor accumulation was limited by 'fast' plasma clearance and 'slow' vascular extravasation. The simple model presented here provides a basic framework to quantitatively understand the blood and tumor pharmacokinetics of ultrasmall NPs under the influence of transient protein interactions.

A protein corona study by scattering correlation spectroscopy: a comparative study between spherical and urchin-shaped gold nanoparticles

The study of protein interactions with gold nanoparticles (GNP) is a key step prior to any biomedical application. These interactions depend on many GNP parameters such as size, surface charge, chemistry, and shape. In this work, we propose to use a sensitive technique named scattering correlation spectroscopy or SCS to study protein interactions with GNP. SCS allowed the investigation of the GNP hydrodynamic radius with a very high sensitivity before and after interaction with proteins. No labeling is needed. As a proof-of-concept, two of the most used morphologies of GNP-based nanovectors have been used within this work: spherical-shaped GNP (GNS) and branched-shaped GNP (GNU). The measurement of several parameters such as the number of proteins binding to one GNP, the binding affinity and the cooperativeness of binding for three different plasma proteins on the GNP surface was carried out. While GNS showed an increase in the hydrodynamic radius, indicating that each kind of protein binds on the GNS in a specific orientation, GNU showed different orientations of proteins due to their multi-oriented surfaces (tips) with a higher surface to volume area. Quantitative data based on the Hill model were extracted to obtain the affinity of the proteins to both GNS and GNU surfaces. Data variations can be understood in terms of the electrostatic properties of the proteins, which interact differently with the negatively charged GNP surfaces.

Allosteric inhibition of α-thrombin enzymatic activity with ultrasmall gold nanoparticles

The catalytic activity of enzymes can be regulated by interactions with synthetic nanoparticles (NPs) in a number of ways. To date, however, the potential use of NPs as allosteric effectors has not been investigated in detail. Importantly, targeting allosteric (distal) sites on the enzyme surface could afford unique ways to modulate the activity, allowing for either enzyme activation, partial or full inhibition. Using p-mercaptobenzoic acid-coated ultrasmall gold NPs (AuMBA) and human α-thrombin as a model system, here we experimentally tested the hypothesis that enzyme activity could be regulated through ultrasmall NP interactions at allosteric sites. We show that AuMBA interacted selectively and reversibly around two positively charged regions of the thrombin surface (exosites 1 and 2) and away from the active site. NP complexation at the exosites transmitted long-range structural changes over to the active site, altering both substrate binding affinity and catalysis. Significantly, thrombin activity was partially reduced - but not completely inhibited - by interactions with AuMBA. These findings indicate that interactions of proteins with ultrasmall NPs may mimic a typical biomolecular complexation event, and suggest the prospect of using ultrasmall particles as synthetic receptors to allosterically regulate protein function.

Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions

A method is described for the efficient simulation of multiprotein systems in crowded environments. It is based on an adaptive, reversible structural coarsening algorithm that preserves relevant physical features of the proteins across scales. Water is treated implicitly whereas all the other components of the aqueous solution, such as ions, cosolutes, or osmolytes, are treated in atomic detail. The focus is on the analytical adaptation of the solvent model to different levels of molecular resolutions, which allows continuous, on-the-fly transitions between scales. This permits the analytical calculation of forces during dynamics and preserves detailed balance in Monte Carlo simulations. A major computational speedup can be achieved in systems containing hundreds of proteins without cutting off the long-range interactions. The method can be combined with a self-adaptive configurational-bias sampling technique described previously, designed to detect strong, weak, or ultra-weak protein associations and shown to improve sampling efficiency and convergence. The implementation aims to simulate early stages of multimeric complexation, aggregation, or self-assembly. The method can be adopted as the basis for a more general algorithm to identify vertices, edges, and hubs in protein interaction networks or to predict critical steps in signal transduction pathways.

Macromolecular crowding for materials-directed controlled self-assembly

Macromolecular crowding refers to intracellular environments where various macromolecules, including proteins and nucleic acids, are present at high total concentrations. Its influence on biological processes has been investigated using a highly concentrated in vitro solution of water-soluble polymers as a model. Studies have revealed significant effects of macromolecular crowding on the thermodynamic equilibria and dynamics of biomolecular self-assembly in vivo. Recently, macromolecular crowding has attracted materials scientists, especially those in bio-related areas, as a tool to control molecular/colloidal self-assembly. Macromolecular crowding has been exploited to control the structure of supramolecular materials, assemble nanomaterials, and improve the performance of polymeric materials. Furthermore, nanostructured materials have been shown to be an interesting alternative to water-soluble polymers for creating crowded environments for controlled self-assembly. In this review article, we summarize recent progress in research on macromolecular crowding for controlled self-assembly in bio-related materials chemistry.

Identification of the binding site between bovine serum albumin and ultrasmall SiC fluorescent biomarkers

Combined experimental and theoretical studies propose a delayed diffusion model for describing the interaction between ultrasmall NPs and proteins.