Fluorescamine Labeling for Assessment of Protein Conformational Change and Binding Affinity in Protein-Nanoparticle Interaction

A comprehensive investigation of the interactions of human serum albumin with polymeric and hybrid nanoparticles

Nanoparticles (NPs) engineered as drug delivery systems continue to make breakthroughs as they offer numerous advantages over free therapeutics. However, the poor understanding of the interplay between the NPs and biomolecules, especially blood proteins, obstructs NP translation to clinics. Nano-bio interactions determine the NPs' in vivo fate, efficacy and immunotoxicity, potentially altering protein function. To fulfill the growing need to investigate nano-bio interactions, this study provides a systematic understanding of two key aspects: (i) protein corona (PC) formation and (ii) NP-induced modifications on protein's structure and stability. A methodology was developed by combining orthogonal techniques to analyze both quantitative and qualitative aspects of nano-bio interactions, using human serum albumin (HSA) as a model protein. Protein quantification via liquid chromatography-mass spectrometry, and capillary zone electrophoresis (CZE) clarified adsorbed protein quantity and stability. CZE further unveiled qualitative insights into HSA forms (native, glycated HSA and cysteinylated), while synchrotron radiation circular dichroism enabled analyzing HSA's secondary structure and thermal stability. Comparative investigations of NP cores (organic vs. hybrid), and shells (with or without polyethylene glycol (PEG)) revealed pivotal factors influencing nano-bio interactions. Polymeric NPs based on poly(lactic-co-glycolic acid) (PLGA) and hybrid NPs based on metal-organic frameworks (nanoMOFs) presented distinct HSA adsorption profiles. PLGA NPs had protein-repelling properties while inducing structural modifications on HSA. In contrast, HSA exhibited a high affinity for nanoMOFs forming a PC altering thereby the protein structure. A shielding effect was gained through PEGylation for both types of NPs, avoiding the PC formation as well as the alteration of unbound HSA structure.

Construction of a New Probe Based on Copper Chaperone Protein for Detecting Cu2+ in Cells

Biomacromolecular probes have been extensively employed in the detection of metal ions for their prominent biocompatibility, water solubility, high selectivity, and easy modification of fluorescent groups. In this study, a fluorescent probe FP was constructed. The probe FP exhibited high specificity recognition for Cu2+. With the combination of Cu2+, the probe was subjected to fluorescence quenching. The research suggested that the probe FP carried out the highly sensitive detection of Cu2+ with detection limits of 1.7 nM. The fluorescence quenching of fluorescamine was induced by Cu2+ perhaps due to the PET (photoinduced electron transfer) mechanism. The FP-Cu2+ complex shows weak fluorescence, which is likely due to the PET quenching effect from Cu2+ to fluorescamine fluorophore. Moreover, the probe FP can be employed for imaging Cu2+ in living cells. The new fluorescent probe developed in this study shows the advantages of good biocompatibility and low cytotoxicity. It can be adopted for the targeted detection of Cu2+ in cells, and it has promising applications in the mechanism research and diagnosis of Cu2+-associated diseases.

Development of a sensitive HPLC method with fluorescence detection for determination of motilin in human plasma

Background: Motilin is a peptide-structured gastrointestinal system hormone. In this study, a sensitive HPLC-fluorescence detection method was developed and validated for the quantification of motilin in human plasma. Materials & methods: Optimization processes were carried out with the experimental design methodology. Analyses were performed on a C8 column (4.6 × 150 mm, 3.5 μm particles) using water and acetonitrile containing trifluoroacetic acid as the mobile phase. Results & conclusion: The method was linear from 2 to 200 ng/ml of motilin. The assay variability was less than 5%. The limit of quantification was found to be 1.84 ng/ml. The applicability of the developed method was successfully demonstrated by quantifying the levels of motilin in human plasma samples.

Selective detection of tartaric acid using amino acid interlinked silver nanoparticles as a colorimetric probe

A variety of biomolecules with different functional groups play critical roles in almost all the processes occurring in living cells. Interaction of metallic nanoparticles (NPs) with various biomolecules generates a layer of molecules on their surface, and this biomolecular rich layer formed on the NP surface is described as a "biomolecular corona". The physicochemical properties of the NPs, including size, adsorption affinity, and charge on the particles' surfaces are the major factors influencing the characteristics of this corona. The formation of various biomolecular corona has been studied well, whereas the amino acid corona is relatively new by exploring their stability. In the present study, a novel formation of an amino acid corona with a fundamental interaction mechanism for a selective detection procedure using a colorimetric platform has been proposed. Herein, amino acid-coated silver NPs (AgNPs) have been used as a template with spectroscopic (steady state UV-Vis, FTIR) and imaging (HR-TEM, DLS) techniques. Our findings demonstrated that among different amino acid coronas, glutathione (GSH) stabilized AgNPs show a rapid reaction with tartaric acid. The extent and thermodynamics of the formed complex between the GSH/AgNPs and tartaric acid have also been studied and this suggested that the complex formed is spontaneous and energy releasing in nature.

Poly(glycidyl methacrylate) macromolecular assemblies as biocompatible nanocarrier for the antimicrobial lysozyme

The antimicrobial lysozyme (Lys) was electrostatically incorporated to negatively charged crosslinked poly(glycidyl methacrylate) (c-PGMA) macromolecular assemblies. The resulting material was characterized by AFM, infrared spectra, water contact angle measurements and the staining with the primary amino specific dye fluorescamine. c-PGMA nanoparticles were successfully loaded with Lys reaching ratios of 27.3 ± 4.0 and 22.5 ± 1.7 mg Lys/g polymer for c-PGMA suspensions and functionalized glass substrates, respectively. Lys-loaded c-PGMA caused clear inhibition zones on S. aureus and E. coli in comparison to neat c-PGMA. c-PGMA functionalized surfaces were intrinsically resistant to colonization, but the incorporation of Lys added resistance to bacterial attachment and allowed keeping surfaces clean of bacterial cells for both strains. A relatively rapid release (24 h) of Lys was observed at physiological pH (7.4). In addition, c-PGMA functionalized substrates could be reloaded several times without losing capacity. c-PGMA macromolecular assemblies did not display cytotoxicity to human dermal fibroblasts as shown in 24 h MTT assays. This work demonstrated that c-PGMA assemblies display durable antibacterial activity, biocompatibility, and full reloading capacity with antimicrobial peptides. c-PGMA functionalized materials have potential application as nanocarriers for anti-infective uses.

Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.

Unfolded Protein Corona Surrounding Nanotubes Influence the Innate and Adaptive Immune System

The plasma proteins around nanoparticles (NPs) form an outer protein corona, significantly influencing the subsequent immune response. However, it was uncertain whether the protein corona around NPs influences immune response. This study clarified that the immune response mediated by the protein corona is greatly dependent on the type of plasma proteins surrounding the NPs. Structural changes in the unfolded protein corona elevated reactive oxygen species (ROS) levels and induced major proinflammatory cytokine release in both murine and human macrophage cell lines. In contrast, negligible structural changes in the protein corona provoke neither ROS production nor proinflammatory cytokine release. Furthermore, in vivo analysis confirms that a stimulated immune response by an unfolded protein corona triggers selective activation of innate and adaptive immunity in the spleen. Specifically, neutrophils, natural killer cells, and CD8+ T cells are overpopulated by unfolded protein corona structures surrounding nanotubes, whereas innate and adaptive immunologic responses are not triggered by a normal protein corona. In conclusion, highly unfolded protein corona structures are strongly correlated with subsequent activation of proinflammatory cytokines and innate immune responses; thus, the protein corona can be used in immune-enhancing therapy.

Fe/Mg-Modified Carbonate Apatite with Uniform Particle Size and Unique Transport Protein-Related Protein Corona Efficiently Delivers Doxorubicin into Breast Cancer Cells

Breast cancer is the abnormal, uncontrollable proliferation of cells in the breast. Conventional treatment modalities like chemotherapy induce deteriorating side effects on healthy cells. Non-viral inorganic nanoparticles (NPs) confer exclusive characteristics, such as, stability, controllable shape and size, facile surface modification, and unique magnetic and optical properties which make them attractive drug carriers. Among them, carbonate apatite (CA) particles are pH-responsive in nature, enabling rapid intracellular drug release, but are typically heterogeneous with the tendency to self-aggregate. Here, we modified the nano-carrier by partially substituting Ca²⁺ with Mg²⁺ and Fe³⁺ into a basic lattice structure of CA, forming Fe/Mg-carbonate apatite (Fe/Mg-CA) NPs with the ability to mitigate self-aggregation, form unique protein corona in the presence of serum and efficiently deliver doxorubicin (DOX), an anti-cancer drug into breast cancer cells. Two formulations of Fe/Mg-CA NPs were generated by adding different concentrations of Fe³⁺ and Mg²⁺ along with a fixed amount of Ca²⁺ in bicarbonate buffered DMEM (Dulbecco's Modified Eagle's Medium), followed by 30 min incubation at 37 °C. Particles were characterized by turbidity analysis, z-average diameter and zeta potential measurement, optical microscopy, field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy (FTIR), energy dispersive X-ray (EDX), flame atomic absorption spectroscopy (FAAS), pH dissolution, drug binding, cellular uptake, thiazolyl blue tetrazolium bromide (MTT) assay, stability analysis, and protein corona study by LCMS (Liquid chromatography-mass spectrometry). Both formulations of Fe/Mg-CA displayed mostly uniform nano-sized particles with less tendency to aggregate. The EDX and FAAS elemental analysis confirmed the weight (%) of Ca, Fe and Mg, along with their Ca/P ratio in the particles. A constant drug binding efficiency was noticed with 5 μM to 10 μM of initial DOX concentration. A pH dissolution study of Fe/Mg-CA NPs revealed the quick release of DOX in acidic pH. Enhancement of cytotoxicity for the chemotherapy drug was greater for Fe/Mg-CA NPs as compared to CA NPs, which could be explained by an increase in cellular internalization as a result of the small z-average diameter of the former. The protein corona study by LCMS demonstrated that Fe/Mg-CA NPs exhibited the highest affinity towards transport proteins without binding with opsonins. Biodistribution study was performed to study the effect of DOX-loaded Fe/Mg-CA NPs on the tissue distribution of DOX in Balb/c 4T1 tumor-bearing mice. Both formulations of Fe/Mg-CA NPs have significantly increased the accumulation of DOX in tumors. Interestingly, high Fe/Mg-CA NPs exhibited less off-target distribution compared to low Fe/Mg-CA NPs. Furthermore, the blood plasma analysis revealed prolonged blood circulation half-life of DOX-loaded low and high Fe/Mg-CA NPs compared to free DOX solution. Modifying CA NPs with Fe³⁺ and Mg²⁺, thereby, led to the generation of nano-sized particles with less tendency to aggregate, enhancing the drug binding efficiency, cellular uptake, and cytotoxicity without hampering drug release in acidic pH, while improving the circulation half-life and tumor accumulation of DOX. Therefore, Fe/Mg-CA which predominantly forms a transport protein-related protein corona could be a proficient carrier for therapeutic delivery in breast cancer.

Prediction of protein corona on nanomaterials by machine learning using novel descriptors

Effective in silico methods to predict protein corona compositions on engineered nanomaterials (ENMs) could help elucidate the biological outcomes of ENMs in biosystems without the need for conducting lengthy experiments for corona characterization. However, the physicochemical properties of ENMs, used as the descriptors in current modeling methods, are insufficient to represent the complex interactions between ENMs and proteins. Herein, we utilized the fluorescence change (FC) from fluorescamine labeling on a protein, with or without the presence of the ENM, as a novel descriptor of the ENM to build machine learning models for corona formation. FCs were significantly correlated with the abundance of the corresponding proteins in the corona on diverse classes of ENMs, including metal and metal oxides, nanocellulose, and 2D ENMs. Prediction models established by the random forest algorithm using FCs as the ENM descriptors showed better performance than the conventional descriptors, such as ENM size and surface charge, in the prediction of corona formation. Moreover, they were able to predict protein corona formation on ENMs with very heterogeneous properties. We believe this novel descriptor can improve in silico studies of corona formation, leading to a better understanding on the protein adsorption behaviors of diverse ENMs in different biological matrices. Such information is essential for gaining a comprehensive view of how ENMs interact with biological systems in ENM safety and sustainability assessments.

Understanding the Chemical Nature of Nanoparticle-Protein Interactions

The formation of a protein corona has been considered a pitfall in the clinical translation of nanomedicines. Hence, interdisciplinary studies on corona characterization are critically essential. A deep understanding of the formation of hard and soft protein coronas upon in vivo administration of nanoparticles is vital. The protein corona gives the nanoplatform a new biological identity. Furthermore, the control of and mechanistic understanding of corona formation as it is regulated by the physicochemical properties of nanoparticles is crucial for developing safe nanomedicines. A growing number of analytical techniques have been developed in the past decade for examining NP-protein interactions, contributing to a better understanding of protein corona formation on the surface of nanoparticles. In this Review, we summarize the latest developments in the in vivo and in vitro study of dynamic protein corona formation. Insights derived from techniques used to visualize, quantify, and define protein coronas, as well as the methods for examining the kinetics and structural changes of coronal proteins, are discussed. The potential challenges and future perspectives in the study of protein corona formation and its effects on biological behavior and applications of therapeutic nanomaterials are also provided.

Visualized detection of apo-transferrin based on cyanine dye supramolecular assembly

In this work, a new biological probe for human transferrin (hTf) detection based on a cyanine dye ETC supramolecular assembly was designed. In sub-micromolar level, apo-hTf could induced the ETC aggregations transferred from H-aggregations to J-band with color change from pink to blue, while holo-hTf hardly possessed the ability, indicating ETC could specifically identify apo-hTf. The present study allowed for apo-hTf detection in the range of 8-80 nM with a detection limit of 2.8 nM and the sensitivity of visualization was around 70 nM. To further examine the suitability, iron ions were added into apo-hTf to stimulate the transformation from open conformation to the closed one gradually. It has been confirmed through tryptophan internal fluorescence quenching and the decrease of ETC J-aggregation. The interaction between ETC and apo-hTf performed high affinity that K_a was reached to 10⁶ M^-1 with a high selectivity. The potential in practical applications of this method has been tested for detection apo-hTf in human serum.

Mapping Molecular Structure of Protein Locating on Nanoparticles with Limited Proteolysis

The molecular structure of a protein could be altered when it is attached to nanoparticles (NPs), affecting the performance of NPs present in biological systems. Limited proteolysis coupled with LC-MS/MS could reveal the changes in protein structure when it binds to a variety of entities, including macro-molecules and small drugs, but it has not yet been applied to study protein-NP interaction. Herein, adsorption of proteins, transferrin, and catalase on the polystyrene (PS) or iron oxide (IO) NPs was analyzed with this method. Both increased and decreased proteolytic efficiency in certain regions on the proteins were observed. Identification of the peptides affected by protein-NP interaction led to proper prediction of alterations to protein function as well as to colloidal stability of NPs. Overall, the present work has demonstrated the utility of limited proteolysis in helping to elucidate the potential biological outcomes of the protein-NP conjugate, obtaining knowledge to guide improvement of the rational design of the protein-conjugated NPs for biomedical applications and to understand the biological behaviors of the engineered NPs.

Formation of Protein Corona on Nanoparticles with Digestive Enzymes in Simulated Gastrointestinal Fluids

The protein corona (PC), which defines the biological identity of nanoparticles in the blood, is well-known, but no comprehensive and systematic study has been conducted yet on the formation of PCs in the gastrointestinal environment. Thus, this study aimed to explore the interaction between model polystyrene nanoparticles (PS-NPs) of 50-100 nm and three digestive enzymes, namely, pepsin, α-amylase, and trypsin. Results showed that the thicknesses of the PCs formed by α-amylase and trypsin were 25-100 and 50-100 nm, respectively. The zeta-potential values of PS-NPs after incubation significantly increased. The fluorescence quenching and ultraviolet-visible-absorption spectra suggested that interactions between the nanoparticles and the enzymes occurred. Synchronous fluorescence spectra showed that the PS-NPs could induce microenvironmental changes in digestive enzymes. The thermodynamic parameters suggested that the interaction was mainly driven by hydrogen bonds and van der Waals forces.

Structure and Interaction of Nanoparticle-Protein Complexes

The integration of nanoparticles with proteins is of high scientific interest due to the amazing potential displayed by their complexes, combining the nanoscale properties of nanoparticles with the specific architectures and functions of the protein molecules. The nanoparticle-protein complexes, in particular, are useful in the emerging field of nanobiotechnology (nanomedicine, drug delivery, and biosensors) as the nanoparticles having sizes comparable to that of living cells can access and operate within the cell. The understanding of nanoparticle interaction with different protein molecules is a prerequisite for such applications. The interaction of the two components has been shown to result in conformational changes in proteins and to affect the surface properties and colloidal stability of the nanoparticles. In this feature article, our recent studies exploring the driving interactions in nanoparticle-protein systems and resultant structures are presented. The anionic colloidal silica nanoparticles and two globular charged proteins [lysozyme and bovine serum albumin (BSA)] have been investigated as model systems. The adsorption behavior of the two proteins on nanoparticles is found to be completely different, but they both give rise to similar phase transformation from one phase to two phase in respective nanoparticle-protein systems. The presence of protein induces the short-range and long-range attraction between the nanoparticles with lysozyme and BSA, respectively. The observed phase behavior and its dependence on various physiochemical parameters (e.g., nanoparticle size, ionic strength, and solution pH) have been explained in terms of underlying interactions.