Biomolecular interactions of ultrasmall metallic nanoparticles and nanoclusters

Thermodynamics and models for small nanoparticles upon protein adsorption

Proteins are some of the most important components in living organisms. When nanoparticles enter a living system, they swiftly interact with proteins to produce the so-called "protein corona", which depicts the adsorption of proteins on large nanoparticles (normally tens to hundreds of nanometers). However, the sizes of small nanoparticles (typically, fluorescent nanomaterials such as quantum dots, noble metal nanoclusters, carbon dots, etc.) are less than 10 nm, which are comparable or even much smaller than those of proteins. Can proteins also adsorb onto the surface of small nanoparticles to form a "protein corona"? In this perspective, the interactions between small nanoparticles with proteins are discussed in detail, including the main characterization methods and thermodynamic mechanisms. The interaction models are summarized. In particular, the concept of a "protein complex" is emphasized.

GraphBNC: Machine Learning-Aided Prediction of Interactions Between Metal Nanoclusters and Blood Proteins

Hybrid nanostructures between biomolecules and inorganic nanomaterials constitute a largely unexplored field of research, with the potential for novel applications in bioimaging, biosensing, and nanomedicine. Developing such applications relies critically on understanding the dynamical properties of the nano-bio interface. This work introduces and validates a strategy to predict atom-scale interactions between water-soluble gold nanoclusters (AuNCs) and a set of blood proteins (albumin, apolipoprotein, immunoglobulin, and fibrinogen). Graph theory and neural networks are utilized to predict the strengths of interactions in AuNC-protein complexes on a coarse-grained level, which are then optimized in Monte Carlo-based structure search and refined to atomic-scale structures. The training data is based on extensive molecular dynamics (MD) simulations of AuNC-protein complexes, and the validating MD simulations show the robustness of the predictions. This strategy can be generalized to any complexes of inorganic nanostructures and biomolecules provided that one generates enough data about the interactions, and the bioactive parts of the nanostructure can be coarse-grained rationally.

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.

Green synthesis of zinc ferrite nanoparticles from Nyctanthes arbor-tristis: unveiling larvicidal potential, protein binding affinity and photocatalytic activities

Environmental pollution, being a major concern worldwide, needs a unique and ecofriendly solution. To answer this, researchers are aiming in utilizing plant extracts for the synthesis of nanoparticles. These NPs synthesized using plant extracts provide a potential, environmentally benign technique for biological and photocatalytic applications. Especially, plant leaf extracts have been safe, inexpensive, and eco-friendly materials for the production of nanoparticles in a greener way. In this work, zinc ferrite nanoparticles (ZnFe2O4 NPs) were prepared using Nyctanthes arbor-tristis leaf extract by hydrothermal method, and its biological and photocatalytic properties were assessed. The synthesized ZnFe2O4 NPs were characterized using powder X-ray diffraction (XRD), scanning electron microscopy (SEM), and Fourier-transform infrared spectroscopy (FT-IR). X-ray diffraction confirmed the arrangement of the fcc crystal structure of the nanoparticles and that some organic substances were encapsulated within the zinc ferrite. According to the SEM analysis, the resulting nanoparticles got agglomerated and spherical in shape. The ZnFe2O4 nanoparticles are in their pure form, and all of their elemental compositions were shown by the energy-dispersive X-ray analysis (EDAX) spectrum. The FTIR results revealed that the produced nanoparticles contained distinctive functional groups. Fluorescence spectroscopy was used to examine the binding affinities between bovine serum albumin (BSA) and ZnFe2O4 nanoparticles in terms of protein binding, stability, and conformation. The interaction between BSA and ZnFe2O4 NPs was examined using steady-state and time-resolved fluorescence measurements, and it was evident that static quenching occurred. The ability of ZnFe2O4 nanoparticles to kill Culex quinquefasciatus (C. quinquefasciatus) larvae was evaluated. The synthesized NPs demonstrated a noteworthy toxic effect against the fourth instar larvae of C. quinquefasciatus with LC50 values of 43.529 µg/mL and LC90 values of 276.867 µg/mL. This study revealed the toxicity of green synthesized ZnFe2O4 NPs on mosquito larvae, proving that these NPs are good and effective larvicides. Furthermore, the ZnFe2O4 NPs were utilized for dye degradation of methylene blue under visible light treatment and achieved 99.5% degradation.

Possibilities and limitations of solution-state NMR spectroscopy to analyze the ligand shell of ultrasmall metal nanoparticles

Ultrasmall nanoparticles have a diameter between 1 and 3 nm at the border between nanoparticles and large molecules. Usually, their core consists of a metal, and the shell of a capping ligand with sulfur or phosphorus as binding atoms. While the core structure can be probed by electron microscopy, electron and powder diffraction, and single-crystal structure analysis for atom-sharp clusters, it is more difficult to analyze the ligand shell. In contrast to larger nanoparticles, ultrasmall nanoparticles cause only a moderate distortion of the NMR signal, making NMR spectroscopy a qualitative as well as a quantitative probe to assess the nature of the ligand shell. The application of isotope-labelled ligands and of two-dimensional NMR techniques can give deeper insight into ligand-nanoparticle interactions. Applications of one- and two-dimensional NMR spectroscopy to analyze ultrasmall nanoparticles are presented with suitable examples, including a critical discussion of the limitations of NMR spectroscopy on nanoparticles.

Stealth and Biocompatible Gold Nanoparticles through Surface Coating with a Zwitterionic Derivative of Glutathione

Gold nanoparticles (AuNPs) hold promise in biomedicine, but challenges like aggregation, protein corona formation, and insufficient biocompatibility must be thoroughly addressed before advancing their clinical applications. Designing AuNPs with specific protein corona compositions is challenging, and strategies for corona elimination, such as coating with polyethylene glycol (PEG), have limitations. In this study, we introduce a commercially available zwitterionic derivative of glutathione, glutathione monoethyl ester (GSHzwt), for the surface coating of colloidal AuNPs. Particles coated with GSHzwt were investigated alongside four other AuNPs coated with various ligands, including citrate ions, tiopronin, glutathione, cysteine, and PEG. We then undertook a head-to-head comparison of these AuNPs to assess their behavior in biological fluid. GSHzwt-coated AuNPs exhibited exceptional resistance to aggregation and protein adsorption. The particles could also be readily functionalized with biotin and interact with streptavidin receptors in human plasma. Additionally, they exhibited significant blood compatibility and noncytotoxicity. In conclusion, GSHzwt provides a practical and easy method for the surface passivation of AuNPs, creating "stealth" particles for potential clinical applications.

Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure

The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.

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.

Multiscale Bioresponses of Metal Nanoclusters

Metal nanoclusters (NCs) are well-recognized novel nano-agents that hold great promise for applications in nanomedicine because of their ultrafine size, low toxicity, and high renal clearance. As foreign substances, however, an in-depth understanding of the bioresponses to metal NCs is necessary but is still far from being realized. Herein, this review is deployed to summarize the biofates of metal NCs at various biological levels, emphasizing their multiscale bioresponses at the molecular, cellular, and organismal levels. In the parts-to-whole schema, the interactions between biomolecules and metal NCs are discussed, presenting typical protein-dictated nano-bio interfaces, hierarchical structures, and in vivo trajectories. Then, the accumulation, internalization, and metabolic evolution of metal NCs in the cellular environment and as-imparted theranostic functionalization are demonstrated. The organismal metabolism and transportation processes of the metal NCs are subsequently distilled. Finally, this review ends with the conclusions and perspectives on the outstanding issues of metal NC-mediated bioresponses in the near future. This review is expected to provide inspiration for tailoring the customization of metal NC-based nano-agents to meet practical requirements in different sectors of nanomedicine.

Ultrastructure and Surface Composition of Glutathione-Terminated Ultrasmall Silver, Gold, Platinum, and Alloyed Silver-Platinum Nanoparticles (2 nm)

Alloyed ultrasmall silver-platinum nanoparticles (molar ratio Ag:Pt = 50:50) were prepared and compared to pure silver, platinum, and gold nanoparticles, all with a metallic core diameter of 2 nm. They were surface-stabilized by a layer of glutathione (GSH). A comprehensive characterization by high-resolution transmission electron microscopy (HRTEM), electron diffraction (ED), X-ray diffraction (XRD), small-angle X-ray scattering (SAXS), differential centrifugal sedimentation (DCS), and UV spectroscopy showed their size both in the dry and in the water-dispersed state (hydrodynamic diameter). Solution NMR spectroscopy (1H, 13C, COSY, HSQC, HMBC, and DOSY) showed the nature of the glutathione shell including the number of GSH ligands on each nanoparticle (about 200 with a molecular footprint of 0.063 nm2 each). It furthermore showed that there are at least two different positions for the GSH ligand on the gold nanoparticle surface. Platinum strongly reduced the resolution of the NMR spectra compared to silver and gold, also in the alloyed nanoparticles. X-ray photoelectron spectroscopy (XPS) showed that silver, platinum, and silver-platinum particles were at least partially oxidized to Ag(+I) and Pt(+II), whereas the gold nanoparticles showed no sign of oxidation. Platinum and gold nanoparticles were well crystalline but twinned (fcc lattice) despite the small particle size. Silver was crystalline in electron diffraction but not in X-ray diffraction. Alloyed silver-platinum nanoparticles were almost fully amorphous by both methods, indicating a considerable internal disorder.

pH-Switchable phenylalanine-templated copper nanoclusters: CO2 probing and efficient peroxidase mimicking activity

Inter-cluster conversion through the strategic tuning of external stimuli and thereby modulation of the optical properties of metal nanoclusters (MNCs) is an emerging domain for exploration. Herein, we report the preparation of blue-emitting CuNCs using phenylalanine (Phe) as a template under acidic conditions (pH ∼ 4). The as-prepared CuNCs exhibit a sequential tuning of the photophysical properties upon varying the pH of the solution from pH ∼4 to pH ∼12. Blue-emitting CuNCs (B-CuNCs, λem = 410 nm) are systematically converted to cyan-emitting CuNCs (C-CuNCs, λem = 490 nm) with a large red-shifted emission maximum by 80 nm as a function of pH. Our present investigation delineates an unprecedented switchability of the photoluminescence (PL) properties of the CuNCs with the variations of the pH from pH ∼4 to pH ∼12. Both the Phe-templated CuNCs (B-CuNCs and C-CuNCs) were broadly characterized by various spectroscopic and morphological techniques. The X-ray photoelectron spectroscopy (XPS) studies reveal the presence of different oxidation states in the metallic core of B-CuNCs and C-CuNCs. These results in turn substantiate the pH-induced intercluster conversion of CuNCs through the substantial change in their core composition as well as valence states. Owing to the pH sensitivity, the CuNCs act as an efficient and highly sensitive probe for CO2, and quantitative estimation of the dissolved CO2 in the form of bicarbonate ions has been achieved through the enhancement of the PL intensity, wherein a very low value of the limit of detection (LOD) of ∼60 μM was obtained. Furthermore, we demonstrated that the CuNCs act as an efficient bio-catalyst with peroxidase mimicking enzymatic activity which has been investigated using OPD as a substrate under physiological conditions (pH ∼7.4 and temperature ∼37 °C). The mechanistic investigations confirmed that the oxidation of OPD mainly proceeds through the generation of hydroxyl radicals (˙OH). We hope the present investigations shed light on a multidimensional aspect of MNCs and uncover an upsurging recent interest in MNCs to act as an artificial enzyme.

An automated interface for sedimentation velocity analysis in SEDFIT

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of suitable software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.

Ultrasmall Gold Nanoparticles as Clients of Biomolecular Condensates

Liquid-liquid phase separation (LLPS) of biopolymers to form condensates is a widespread phenomenon in living cells. Agents that target or alter condensation can help uncover elusive physiological and pathological mechanisms. Owing to their unique material properties and modes of interaction with biomolecules, nanoparticles represent attractive condensate-targeting agents. Our work focused on elucidating the interaction between ultrasmall gold nanoparticles (usGNPs) and diverse types of condensates of tau, a representative phase-separating protein associated with neurodegenerative disorders. usGNPs attract considerable interest in the biomedical community due to unique features, including emergent optical properties and good cell penetration. We explored the interaction of usGNPs with reconstituted self-condensates of tau, two-component tau/polyanion and three-component tau/RNA/alpha-synuclein coacervates. The usGNPs were found to concentrate into condensed liquid droplets, consistent with the formation of dynamic client (nanoparticle) - scaffold (tau) interactions, and were observable thanks to their intrinsic luminescence. Furthermore, usGNPs were capable to promote LLPS of a protein domain which is unable to phase separate on its own. Our study demonstrates the ability of usGNPs to interact with and illuminate protein condensates. We anticipate that nanoparticles will have broad applicability as nanotracers to interrogate phase separation, and as nanoactuators controlling the formation and dissolution of condensates.

An automated interface for sedimentation velocity analysis in SEDFIT

Sedimentation velocity analytical ultracentrifugation (SV-AUC) is an indispensable tool for the study of particle size distributions in biopharmaceutical industry, for example, to characterize protein therapeutics and vaccine products. In particular, the diffusion-deconvoluted sedimentation coefficient distribution analysis, in the software SEDFIT, has found widespread applications due to its relatively high resolution and sensitivity. However, a lack of available software compatible with Good Manufacturing Practices (GMP) has hampered the use of SV-AUC in this regulatory environment. To address this, we have created an interface for SEDFIT so that it can serve as an automatically spawned module with controlled data input through command line parameters and output of key results in files. The interface can be integrated in custom GMP compatible software, and in scripts that provide documentation and meta-analyses for replicate or related samples, for example, to streamline analysis of large families of experimental data, such as binding isotherm analyses in the study of protein interactions. To test and demonstrate this approach we provide a MATLAB script mlSEDFIT.

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.

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.

Silencing of proinflammatory NF-κB and inhibition of herpes simplex virus (HSV) replication by ultrasmall gold nanoparticles (2 nm) conjugated with small-interfering RNA

Azide-terminated ultrasmall gold nanoparticles (2 nm gold core) were covalently functionalized with alkyne-terminated small-interfering siRNA duplexes by copper-catalyzed azide-alkyne cycloaddition (CuAAC; click chemistry). The nanoparticle core was visualized by transmission electron microscopy. The number of attached siRNA molecules per nanoparticle was determined by a combination of atomic absorption spectroscopy (AAS; for gold) and UV-Vis spectroscopy (for siRNA). Each nanoparticle carried between 6 and 10 siRNA duplex molecules which corresponds to a weight ratio of siRNA to gold of about 2.2 : 1. Different kinds of siRNA were conjugated to the nanoparticles, depending on the gene to be silenced. In general, the nanoparticles were readily taken up by cells and highly efficient in gene silencing, in contrast to free siRNA. This was demonstrated in HeLa-eGFP cells (silencing of eGFP) and in LPS-stimulated macrophages (silencing of NF-κB). Furthermore, we demonstrated that nanoparticles carrying antiviral siRNA potently inhibited the replication of Herpes simplex virus 2 (HSV-2) in vitro. This highlights the strong potential of siRNA-functionalized ultrasmall gold nanoparticles in a broad spectrum of applications, including gene silencing and treatment of viral infections, combined with a minimal dose of gold.

A Combinatorial Study Investigating the Growth of Ultrasmall Embedded Silver Nanoparticles upon Thermal Annealing

Ultrasmall nanoparticles (NPs) with a high active surface area are essential for optoelectronic and photovoltaic applications. However, the structural stability and sustainability of these ultrasmall NPs at higher temperatures remain a critical problem. Here, we have synthesized the nanocomposites (NCs) of Ag NPs inside the silica matrix using the atom beam co-sputtering technique. The post-deposition growth of the embedded Ag NPs is systematically investigated at a wide range of annealing temperatures (ATs). A novel, fast, and effective procedure, correlating the experimental (UV-vis absorption results) and theoretical (quantum mechanical modeling, QMM) results, is used to estimate the size of NPs. The QMM-based simulation, employed for this work, is found to be more accurate in reproducing the absorption spectra over the classical/modified Drude model, which fails to predict the expected shift in the LSPR for ultrasmall NPs. Unlike the classical Drude model, the QMM incorporates the intraband transition of the conduction band electrons to calculate the effective dielectric function of metallic NCs, which is the major contribution of LSPR shifts for ultrasmall NPs. In this framework, a direct comparison is made between experimentally and theoretically observed LSPR peak positions, and it is observed that the size of NPs grows from 3 to 18 nm as AT increases from room temperature to 900 °C. Further, in situ grazing-incidence small- & wide-angle X-ray scattering and transmission electron microscopy measurements are employed to comprehend the growth of Ag NPs and validate the UV + QMM results. We demonstrate that, unlike chemically grown NPs, the embedded Ag NPs ensure greater stability in size and remain in an ultrasmall regime up to 800 °C, and beyond this temperature, the size of NPs increases exponentially due to dominant Ostwald ripening. Finally, a three-stage mechanism is discussed to understand the process of nucleation and growth of the silica-embedded Ag NPs.

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.

High-Throughput Colorimetric Analysis of Nanoparticle-Protein Interactions Based on the Enzyme-Mimic Properties of Nanoparticles

While an in-depth understanding of the biological behavior of engineered nanoparticles (NPs) is of great importance for their various applications, it remains challenging to quantitatively characterize NP-protein interactions in a simple and high-throughput manner. In the present work, we propose a new, colorimetric approach capable of quantitatively analyzing the adsorption of proteins onto the surface of NPs by their distinct peroxidase-mimic properties. Taking cationic AuNPs as an example, we demonstrate that this colorimetric method is capable of evaluating NP-protein interactions in a simple and high-throughput manner in multiwell plates. Important binding parameters (e.g., the binding affinity) of three different serum proteins (bovine serum albumin, transferrin, and lysozyme) as well as human serum to AuNPs with three different sizes (average diameters of 5, 10, and 15 nm) have been obtained. Based on a quantitative analysis of NP-protein interactions, we observe that the binding affinity and the inhibition efficiency of the nanozyme activity of AuNPs are strongly affected by the characteristics of proteins as well as the sizes of NPs. These results illustrate the great potential of the present colorimetric method as a simple, low-cost, and high-throughput platform for quantitatively investigating NP-protein interactions.

Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides

Computational design of antimicrobial peptides (AMPs) is a promising area of research for developing novel agents against drug-resistant bacteria. AMPs are present naturally in many organisms, from bacteria to humans, a time-tested mechanism that makes them attractive as effective antibiotics. Depending on the environment, AMPs can exhibit α-helical or β-sheet conformations, a mix of both, or lack secondary structure; they can be linear or cyclic. Prediction of their structures is challenging but critical for rational design. Promising AMP leads can be developed using essentially two approaches: traditional modeling of the physicochemical mechanisms that determine peptide behavior in aqueous and membrane environments and knowledge-based, e.g., machine learning (ML) techniques, that exploit ever-growing AMP databases. Here, we explore the conformational landscapes of two recently ML-designed AMPs, characterize the dependence of these landscapes on the medium conditions, and identify features in peptide and membrane landscapes that mediate protein-membrane association. For both peptides, we observe greater conformational diversity in an aqueous solvent than in a less polar solvent, and one peptide is seen to alter its conformation more dramatically than the other upon the change of solvent. Our results support the view that structural rearrangement in response to environmental changes is central to the mechanism of membrane-structure disruption by linear peptides. We expect that the design of AMPs by ML will benefit from the incorporation of peptide conformational substates as quantified here with molecular simulations.

Covalent Attachment of Aggregation-Induced Emission Molecules to the Surface of Ultrasmall Gold Nanoparticles to Enhance Cell Penetration

Three different alkyne-terminated aggregation-induced emission molecules based on a para-substituted di-thioether were attached to the surface of ultrasmall gold nanoparticles (2 nm) by copper-catalyzed azide–alkyne cycloaddition (click chemistry). They showed a strong fluorescence and were well water-dispersible, in contrast to the dissolved AIE molecules. The AIE-loaded nanoparticles were not cytotoxic and easily penetrated the membrane of HeLa cells, paving the way for an intracellular application of AIE molecules, e.g., for imaging.

Evaluation of noble metal nanostructure-serum albumin interactions in 2D and 3D systems: Thermodynamics and possible mechanisms

In this review, we clearly highlight the importance of the detailed study of the interactions between noble metal colloids (nanoparticles (NPs) and nanoclusters (NCs)) with serum albumins (SAs) due to their rapidly growing presence in biomedical research. Besides the changes in the structure and optical property of SA, we demonstrate that the characteristic localized surface plasmon resonance (LSPR) feature of the colloidal noble metal NPs and the size- and structure-dependent photoluminescence (PL) property of the sub-nanometer sized NCs are also altered differently because of the interactions between them. Namely, for plasmonic NPs - SA interactions the PL quenching of SA (mainly static) is identified, while the SA cause PL enhancement of the ultra-small NCs after complexation. This review summarizes that the thermodynamic nature and the possible mechanisms of the binding processes are dependent partly on the size, morphology, and type of the noble metals, while the chemical structure as well as the charge of the stabilizing ligands have the most dominant effect on the change in optical features. In addition to the thermodynamic data and proposed binding mechanisms provided by three-dimensional spectroscopic techniques, the quantitative and real-time data of "quasi" two-dimensional sensor apparatus should also be considered to provide a comprehensive evaluation on many aspects of the particle/cluster - SA interactions.

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.

Evaluation of Phoma sp. Biomass as an Endophytic Fungus for Synthesis of Extracellular Gold Nanoparticles with Antibacterial and Antifungal Properties

The aim of our study was to examine the different concentrations of AuNPs as a new antimicrobial substance to control the pathogenic activity. The extracellular synthesis of AuNPs performed by using Phoma sp. as an endophytic fungus. Endophytic fungus was isolated from vascular tissue of peach trees (Prunus persica) from Baft, located in Kerman province, Iran. The UltraViolet-Visible Spectroscopy (UV-Vis spectroscopy) and Fourier transform infrared spectroscopy provided the absorbance peak at 526 nm, while the X-ray diffraction and transmission electron microscopy images released the formation of spherical AuNPs with sizes in the range of 10-100 nm. The findings of inhibition zone test of Au nanoparticles (AuNPs) showed a desirable antifungal and antibacterial activity against phytopathogens including Rhizoctonia solani AG1-IA (AG1-IA has been identified as the dominant anastomosis group) and Xanthomonas oryzae pv. oryzae. The highest inhibition level against sclerotia formation was 93% for AuNPs at a concentration of 80 μg/mL. Application of endophytic fungus biomass for synthesis of AuNPs is relatively inexpensive, single step and environmentally friendly. In vitro study of the antifungal activity of AuNPs at concentrations of 10, 20, 40 and 80 μg/mL was conducted against rice fungal pathogen R. solani to reduce sclerotia formation. The experimental data revealed that the Inhibition rate (RH) for sclerotia formation was (15, 33, 74 and 93%), respectively, for their corresponding AuNPs concentrations (10, 20, 40 and 80 μg/mL). Our findings obviously indicated that the RH strongly depend on AuNPs rates, and enhance upon an increase in AuNPs rates. The application of endophytic fungi biomass for green synthesis is our future goal.

Interactions of cationic gold nanoclusters with serum proteins and effects on their cellular responses

Cationic nanoparticles (NPs) have shown great potential in biological applications owing to their distinct features such as favorable cellular internalization and easy binding to biomolecules. However, our current knowledge of cationic NPs' biological behavior, i.e., NP-protein interactions, is still rather limited. Herein, we choose ultrasmall-sized fluorescent gold nanoclusters (AuNCs) coated by (11-mercaptoundecyl) - N, N, N - trimethylammonium bromide (MUTAB) as representative cationic NPs, and systematically study their interactions with different serum proteins at nano-bio interfaces. By monitoring the fluorescence intensity of MUTAB-AuNCs, all proteins are observed to bind with roughly micromolar affinities to AuNCs and quench their fluorescence. Transient fluorescence spectroscopy, X-ray photoelectron spectroscopy and isothermal titration calorimetry are also adopted to characterize the physicochemical properties of MUTAB-AuNCs after the protein adsorption. Concomitantly, circular dichroism spectroscopy reveals that cationic AuNCs can exert protein-dependent conformational changes of these serum proteins. Moreover, protein adsorption onto cationic AuNCs can significantly influence their cellular responses such as cytotoxicity and uptake efficiency. These results provide important knowledge towards understanding the biological behaviors of cationic nanoparticles, which will be helpful in further designing and utilizing them for safe and efficient biomedical applications.

Regulation of the Enzymatic Activities of Lysozyme by the Surface Ligands of Ultrasmall Gold Nanoclusters: The Role of Hydrophobic Interactions

Nanomaterials for biological applications would inevitably encounter and interact with biomolecules, which have a profound impact on the properties, functions, and even fates of both nanomaterials and biomolecules. Among the biomolecules, lysozyme (Lys) is of great importance in defending the bacterial intruder and maintaining health. Here, the interactions between fluorescent gold nanoclusters (AuNCs) (∼2 nm) capped with different surface ligands and Lys were thoroughly investigated. Fluorescence spectroscopic studies showed that dihydrolipoic acid (DHLA)-capped and glutathione (GSH)-capped AuNCs both quenched the intrinsic fluorescence of Lys by different quenching mechanisms. Agarose gel electrophoresis and zeta-potential assays showed that statistically one DHLA-AuNC could bind one Lys, while one GSH-AuNC could bind 3-4 Lys, providing new examples for the concept of a "protein complex". Activity assays indicated that DHLA-AuNCs heavily inhibited the enzymatic activity of Lys, while GSH-AuNCs had little effect. By synchronous fluorescence and circular dichroism spectroscopic studies, it was deduced that both AuNCs would interact with Lys by electrostatic attractions due to the distinct surface charges, and then DHLA-AuNCs would further interact with Lys by hydrophobic interactions, probably due to the hydrophobic carbon chain of DHLA and the hydrophobic side chains of amino acid residues in Lys, which was proved by the significant secondary structure changes caused by DHLA-AuNCs. Meanwhile, conformational changes induced by GSH-AuNCs with zwitterionic ligands were neglectable. Therefore, this work provided a comprehensive study of the consequences and mechanisms of the interactions between Lys and AuNCs, which was essential for the design and better use of nanomaterials as biological agents.

Current approaches for the exploration of antimicrobial activities of nanoparticles

Infectious diseases of bacterial and viral origins contribute to substantial mortality worldwide. Collaborative efforts have been underway between academia and the industry to develop technologies for a more effective treatment for such diseases. Due to their utility in various industrial applications, nanoparticles (NPs) offer promising potential as antimicrobial agents against bacterial and viral infections. NPs have been established to possess potent antimicrobial activities against various types of pathogens due to their unique characteristics and cell-damaging ability through several mechanisms. The recently accepted antimicrobial mechanisms possessed by NPs include metal ion release, oxidative stress induction, and non-oxidative mechanisms. Another merit of NPs lies in the low likelihood of the development of microbial tolerance towards NPs, given the multiple simultaneous mechanisms of action against the pathogens targeting numerous gene mutations in these pathogens. Moreover, NPs provide a fascinating opportunity to curb microbial growth before infections: this outstanding feature has led to their utilization as active antimicrobial agents in different industrial applications, e.g. the coating of medical devices, incorporation in food packaging, promoting wound healing and encapsulation with other potential materials for wastewater treatment. This review discusses the progress and achievements in the antimicrobial applications of NPs, factors contributing to their actions, mechanisms underlying their efficiency, and risks of their applications, including the antimicrobial action of metal nanoclusters (NCs). The review concludes with a discussion of the restrictions on present studies and future prospects of nanotechnology-based NPs development.