Rapid insight into C60 influence on biological functions of proteins

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.

Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies

Fullerenes, particularly C60, exhibit unique properties that make them promising candidates for various applications, including drug delivery and nanomedicine. However, their interactions with biomolecules, especially proteins, remain not fully understood. This study implements both explicit and implicit C60 models into the UNRES coarse-grained force field, enabling the investigation of fullerene-protein interactions without the need for restraints to stabilize protein structures. The UNRES force field offers computational efficiency, allowing for longer timescale simulations while maintaining accuracy. Five model proteins were studied: FK506 binding protein, HIV-1 protease, intestinal fatty acid binding protein, PCB-binding protein, and hen egg-white lysozyme. Molecular dynamics simulations were performed with and without C60 to assess protein stability and investigate the impact of fullerene interactions. Analysis of contact probabilities reveals distinct interaction patterns for each protein. FK506 binding protein (1FKF) shows specific binding sites, while intestinal fatty acid binding protein (1ICN) and uteroglobin (1UTR) exhibit more generalized interactions. The explicit C60 model shows good agreement with all-atom simulations in predicting protein flexibility, the position of C60 in the binding pocket, and the estimation of effective binding energies. The integration of explicit and implicit C60 models into the UNRES force field, coupled with recent advances in coarse-grained modeling and multiscale approaches, provides a powerful framework for investigating protein-nanoparticle interactions at biologically relevant scales without the need to use restraints stabilizing the protein, thus allowing for large conformational changes to occur. These computational tools, in synergy with experimental techniques, can aid in understanding the mechanisms and consequences of nanoparticle-biomolecule interactions, guiding the design of nanomaterials for biomedical applications.

Recent advances in supramolecular fullerene chemistry

Fullerene chemistry has come a long way since 1990, when the first bulk production of C60 was reported. In the past decade, progress in supramolecular chemistry has opened some remarkable and previously unexpected opportunities regarding the selective (multiple) functionalization of fullerenes and their (self)assembly into larger structures and frameworks. The purpose of this review article is to provide a comprehensive overview of these recent developments. We describe how macrocycles and cages that bind strongly to C60 can be used to block undesired addition patterns and thus allow the selective preparation of single-isomer addition products. We also discuss how the emergence of highly shape-persistent macrocycles has opened opportunities for the study of photoactive fullerene dyads and triads as well as the preparation of mechanically interlocked compounds. The preparation of two- or three-dimensional fullerene materials is another research area that has seen remarkable progress over the past few years. Due to the rapidly decreasing price of C60 and C70, we believe that these achievements will translate into all fields where fullerenes have traditionally (third-generation solar cells) and more recently been applied (catalysis, spintronics).

Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking

Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.

Removal of carboxylated multi-walled carbon nanotubes (MWCNT-COOH) from the environment by Trametes versicolor: a simple, cost-effective, and eco-friendly method

Nanotechnology has increased the release of nanoparticles into the environment, which poses a risk to human health and the ecosystem. Therefore, finding ways to eliminate these hazardous particles from the environment is crucial. This research studied the ability of Trametes versicolor fungi to remove carboxylated multi-walled carbon nanotubes. The study analyzed the impact of pH, MWCNT-COOH concentration, and initial fungal growth time on the removal process. The properties of the adsorbent were measured before and after the biosorption process using SEM, FTIR, and EDS techniques. The results showed that the live biomass of T. versicolor was more effective in removing nanoparticles than dead biomass at 30 °C and pH 7. An increase in carbon nanotube concentration from 5 to 20 mg. mL-1 decreased biosorption potential from 100% to 28.55 ± 1.7%. The study also found that an increase in initial fungal growth time led to higher biomass production and adsorption capacity, increasing biosorption ability for concentrations > 5mg. ml-1. The biosorption kinetics followed a pseudo-second-order model and corresponded most closely to the Freundlich isotherm model. The adsorption capacity of live fungal biomass to remove multi-walled carbon nanotubes was 945.17 mg. g-1, indicating that T. versicolor fungi have significant potential for removing carbon nanostructures from the environment.

Interfacial Hyperactivation of Candida rugosa Lipase onto Ca2Fe2O5 Nanoparticles: pH and Ionic Strength Fine-Tuning to Modulate Protein-Support Interactions

The current study provides a comprehensive look of the adsorption process of Candida rugosa lipase (CRL) on Ca2Fe2O5 iron oxide nanoparticles (NPs). Protein-support interactions were identified across a broad range of pH and ionic strengths (mM) through a response surface methodology, surface charge determination, and spectroscopic and in silico analyses. The maximum quantity of immobilized protein was achieved at an ionic strength of 50 mM and pH 4. However, this condition did not allow for the greatest hydrolytic activity to be obtained. Indeed, it was recorded at acidic pH, but at 150 mM, where evaluation of the recovered activity revealed hyperactivation of the enzyme. These findings were supported by adsorption isotherms performed under different conditions. Based on zeta potential measurements, electrostatic interactions contributed differently to protein-support binding under the conditions tested, showing a strong correlation with experimentally determined immobilization parameters. Raman spectra revealed an increase in hydrophobicity around tryptophan residues, whereas the enzyme immobilization significantly reduced the phenylalanine signal in CRL. This suggests that this residue was involved in the interaction with Ca2Fe2O2 and molecular docking analysis confirmed these findings. Fluorescence spectroscopy showed distinct behaviors in the CRL emission patterns with the addition of Ca2Fe2O5 at pH 4 and 7. The calculated thermodynamic parameters indicated that the contact would be mediated by hydrophobic interactions at both pHs, as well as by ionic ones at pH 4. In this approach, this work adds to our understanding of the design of biocatalysts immobilized in iron oxide NPs.

Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation

Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.

Enhanced Uptake and Phototoxicity of C60@albumin Hybrids by Folate Bioconjugation

Fullerenes are considered excellent photosensitizers, being highly suitable for photodynamic therapy (PDT). A lack of water solubility and low biocompatibility are, in many instances, still hampering the full exploitation of their potential in nanomedicine. Here, we used human serum albumin (HSA) to disperse fullerenes by binding up to five fullerene cages inside the hydrophobic cavities. Albumin was bioconjugated with folic acid to specifically address the folate receptors that are usually overexpressed in several solid tumors. Concurrently, tetramethylrhodamine isothiocyanate, TRITC, a tag for imaging, was conjugated to C₆₀@HSA in order to build an effective phototheranostic platform. The in vitro experiments demonstrated that: (i) HSA disperses C₆₀ molecules in a physiological environment, (ii) HSA, upon C₆₀ binding, maintains its biological identity and biocompatibility, (iii) the C₆₀@HSA complex shows a significant visible-light-induced production of reactive oxygen species, and (iv) folate bioconjugation improves both the internalization and the PDT-induced phototoxicity of the C₆₀@HSA complex in HeLa cells.

Effects of biochar-based materials on the bioavailability of soil organic pollutants and their biological impacts

Motivated by the unique structure and superior properties, biochar-based materials, including pristine biochar and composites of biochar with other functional materials, are considered as new generation materials for diverse multi-functional applications, which may be intentionally or unintentionally released to soil. The influencing mechanism of biochar-based material on soil organisms is a key aspect for quantifying and predicting its benefits and trade-offs. This work focuses on the effects of biochar-based materials on soil organisms within the past ten years. 206 sources are reviewed and available knowledge on biochar-based materials' impacts on soil organisms is summarized from a diverse perspective, including the pollutant bioavailability changes in soil, and potential effects of biochar-based materials on soil organisms. Herein, effects of biochar-based materials on the bioavailability of soil organic pollutants are detailed, from the perspective of plant, microorganism, and soil fauna. Potential biological effects of pristine biochar (PBC), metal/metal compounds-biochar composites (MBC), clay minerals-biochar composites (CMBC), and carbonaceous materials-biochar composites (CBC) on soil organisms are highlighted for the first time. And possible mechanisms are presented based on the different characters of biochar-based materials as well as various environmental interactions. Finally, the bottleneck and challenges of risk assessment of biochar-based materials as well as future prospects are proposed. This work not only promotes the development of risk assessment system of biochar-based materials, but broadens the strategy for the design and optimization of environmental-friendly biochar materials.

Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C₆₀. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol⁻¹, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol⁻¹ for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C₆₀ was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C₆₀ binding.

Nano-cell and nano-pollutant interactions constitute key elements in nanoparticle-pollutant combined cytotoxicity

As the wide application of carbon nanoparticles (CNPs) and zinc oxide nanoparticles (ZnONPs), as well as ubiquitous chromium (Cr(VI)) pollution in environment, the chance of human exposure to CNPs/ZnONPs and their Cr(VI) adducts is enhanced. We therefore investigated the impacts of nano-cell and nano-Cr(VI) interactions on nanoparticle-Cr(VI) combined cytotoxicity in human lung epithelial (A549) cells. Our results showed that nano-cell and nano-pollutant interactions were the key elements in NP-pollutant combined cytotoxicity, as determined by cell death, oxidative stress and mitochondrial dysfunction. A strong adsorption of Cr(VI) on CNPs and reduction of Cr(VI) to Cr(III) were confirmed, resulting in the reduced cytotoxicity of CNP-Cr(VI) adducts. In contrast, ZnONPs caused the destruction of cell membranes so that more ZnONP-Cr(VI) adducts could enter the cells. Meantime, more Cr contents could be released from ZnONP-Cr(VI) adducts once entering cells and locating in lysosomes than that from CNP-Cr(VI) adducts. These two reasons together caused the enhanced cytotoxicity of ZnONP-Cr(VI) adducts. These findings indicate that the in-depth investigations on the interaction mechanisms are crucial to comprehensively understand the combined cytotoxicity of different NPs and pollutants.

Toxicological Aspects of Carbon Nanotubes, Fullerenes and Graphenes

Nanomedicines exhibit unbelievable capability in overcoming the hurdles faced in biological applications. Carbon nanotubes (CNTs), graphene-family nanomaterials and fullerenes are a class of engineered nanoparticles that have emerged as a new option for possible use in drug/gene delivery for life-threatening diseases. Their adaptability to pharmaceutical applications has opened new vistas for biomedical applications. Successful applications of this family of engineered nanoparticles in various fields may not support their use in medicine due to inconsistent data on toxicity as well as the lack of a centralized toxicity database. Inconsistent toxicological studies and lack of mechanistic understanding have been the reasons for limited understanding of their toxicological aspects. These nanoparticles, when underivatized or pristine, are considered as safe, however less reactive. The derivatized forms or functionalization changes their chemistry significantly to modify their biological effects including toxicity. They can cause acute and long term injuries in tissues by penetration through the the blood-air barrier, blood-alveolus barrier, blood-brain barrier, and blood-placenta barrier. and by accumulating in the lung, liver, and spleen . The toxicological effects are manifested through inflammatory response, DNA damage, apoptosis, autophagy and necrosis. Other factors that largely influence the toxicity of carbon nanotubes, graphenes and fullerenes are the concentration, functionalization, dimensional and surface topographical factors. Thus, a better understanding of the toxicity profile of CNTs, graphene-family nanomaterials and fullerenes in humans, animals and the environment is of significant importance, to improve their biological safety, to facilitate their wide biological application and for the successful commercial application. The exploration of appropriate cell lines to investigate specific receptors and intracellular targets as well as chronic toxicity beyond the proof-of-concept is required.

Antagonistic cytoprotective effects of C60 fullerene nanoparticles in simultaneous exposure to benzo[a]pyrene in a molluscan animal model

The hypothesis that C₆₀ fullerene nanoparticles (C₆₀) exert an antagonistic interactive effect on the toxicity of benzo[a]pyrene (BaP) has been supported by this investigation. Mussels were exposed to BaP (5, 50 & 100μg/L) and C₆₀ (C₆₀-1mg/L) separately and in combination. Both BaP and C₆₀ were shown to co-localize in the secondary lysosomes of the hepatopancreatic digestive cells in the digestive gland where they reduced lysosomal membrane stability (LMS) or increased membrane permeability, while BaP also induced increased lysosomal lipid and lipofuscin, indicative of oxidative cell injury and autophagic dysfunction. Combinations of BaP and C₆₀ showed antagonistic effects for lysosomal stability, mTORC1 (mechanistic target of rapamycin complex 1) inhibition and intralysosomal lipid (5 & 50μg/L BaP). The biomarker data (i.e., LMS, lysosomal lipidosis and lipofuscin accumulation; lysosomal/cell volume and dephosphorylation of mTORC1) were further analysed using multivariate statistics. Principal component and cluster analysis clearly indicated that BaP on its own was more injurious than in combination with C₆₀. Use of a network model that integrated the biomarker data for the cell pathophysiological processes, indicated that there were significant antagonistic interactions in network complexity (% connectance) at all BaP concentrations for the combined treatments. Loss of lysosomal membrane stability probably causes the release of intralysosomal iron and hydrolases into the cytosol, where iron can generate harmful reactive oxygen species (ROS). It was inferred that this adverse oxidative reaction induced by BaP was ameliorated in the combination treatments by the ROS scavenging property of intralysosomal C₆₀, thus limiting the injury to the lysosomal membrane; and reducing the oxidative damage in the cytosol and to the nuclear DNA. The ROS scavenging by C₆₀, in combination with enhanced autophagic turnover of damaged cell constituents, appeared to have a cytoprotective effect against the toxic reaction to BaP in the combined treatments.

Investigating the Size-Dependent Binding of Pristine nC60 to Bovine Serum Albumin by Multi-Spectroscopic Techniques

The morphology of nanomaterials may affect their interaction with biomacromolecules such as proteins. Previous work has studied the size-dependent binding of pristine nC₆₀ to bovine/human serum albumin using the fluorometric method and found that the fluorescence inner filter effect might affect this interaction. However, if it is necessary to accurately calculate and obtain binding information, the fluorescence inner filter effect should not be ignored. This work aimed to further investigate the effect of the fluorescence inner filter on the interaction between pristine nC₆₀ with different particle sizes (140–160, 120–140, 90–110, 50–70, and 30–50 nm) and bovine serum albumin for a more accurate comprehension of the binding of pristine nC₆₀ to bovine serum albumin. The nC₆₀ nanoparticles with different size distributions used in the experiments were obtained by the solvent displacement and centrifugation method. UV-Vis spectroscopy and fluorescence spectroscopy were used to study the binding of nC₆₀ with different size distributions to bovine serum albumin (BSA) before and after eliminating the fluorescence inner filter effect. The results showed that the fluorescence inner filter effect had an influence on the interaction between nC₆₀ and proteins to some extent, and still did not change the rule of the size-dependent binding of nC₆₀ nanoparticles to BSA. Further studies on the binding parameters (binding constants and the number of binding sites) between them were performed, and the effect of the binding on BSA structures and conformation were also speculated.

Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation

Carbon nanoparticles (CNPs) are attractive materials for a great number of applications but there are serious concerns regarding their influence on health and environment. Here, our focus is on the behavior of fullerenes in lipid bilayers with varying lipid saturations, chain lengths and fullerene concentrations using coarse-grained molecular dynamics (CG-MD) simulations. Our findings show that the lipid saturation level is a key factor in determining how fullerenes behave and where the fullerenes are located inside a lipid bilayer. In saturated and monounsaturated bilayers fullerenes aggregated and formed clusters with some of them showing icosahedral structures. In polyunsaturated lipid bilayers, no such structures were observed: In polyunsaturated lipid bilayers at high fullerene concentrations, connected percolation-like networks of fullerenes spanning the whole lateral area emerged at the bilayer center. In other systems only separate isolated aggregates were observed. The effects of fullerenes on lipid bilayers depend strongly on fullerene aggregation. When fullerenes aggregate, their interactions with the lipid tails change.

Advances in the application, toxicity and degradation of carbon nanomaterials in environment: A review

Carbon nanomaterials (CNMs) are novel nanomaterials with excellent physicochemical properties, which are widely used in biomedicine, energy and sensing. Besides, CNMs also play an important role in environmental pollution control, which can absorb heavy metals, antibiotics and harmful gases. However, CNMs are inevitably entering the environment while they are rapidly developing. They are harmful to living organisms in the environment and are difficult to degrade under natural conditions. Here, we systematically describe the toxicity of carbon nanotubes (CNTs), graphene (GRA) and C₆₀ to cells, animals, humans, and microorganisms. According to the current research results, the toxicity mechanism is summarized, including oxidative stress response, mechanical damage and effects on biological enzymes. In addition, according to the latest research progress, we focus on the two major degradation methods of chemical degradation and biodegradation of CNTs, GRA and C₆₀. Meanwhile, the reaction conditions and degradation mechanisms of degradation are respectively stated. Moreover, we have prospects for the limitations of CNM degradation under non-experimental conditions and their potential application.

Triplet Fullerenes as Prospective Spin Labels for Nanoscale Distance Measurements by Pulsed Dipolar EPR Spectroscopy

Precise nanoscale distance measurements by pulsed electron paramagnetic resonance (EPR) spectroscopy play a crucial role in structural studies of biomolecules. The properties of the spin labels used in this approach determine the sensitivity limits, attainable distances, and proximity to biological conditions. Herein, we propose and validate the use of photoexcited fullerenes as spin labels for pulsed dipolar (PD) EPR distance measurements. Hyperpolarization and the narrower spectrum of fullerenes compared to other triplets (e.g., porphyrins) boost the sensitivity, and superior relaxation properties allow PD EPR measurements up to a near-room temperature. This approach is demonstrated using fullerene-nitroxide and fullerene-triarylmethyl pairs, as well as a supramolecular complex of fullerene with nitroxide-labeled protein. Photoexcited triplet fullerenes can be considered as new spin labels with outstanding spectroscopic properties for future structural studies of biomolecules.

Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins

With the advances in three-dimensional structure determination techniques, high quality structures of the iron transport proteins transferrin and the bacterial ferric binding protein (FbpA) have been deposited in the past decade. These are proteins of relatively large size, and developments in hardware and software have only recently made it possible to study their dynamics using standard computational resources. We review computational techniques towards understanding the equilibrium and kinetic properties of iron transport proteins under different environmental conditions. At the level of detail that requires quantum chemical treatments, the octahedral geometry around iron has been scrutinized and it has been established that the iron coordinating tyrosines are in an unusual deprotonated state. At the atomistic level, both the N-lobe and the full bilobal structure of transferrin have been studied under varying conditions of pH, ionic strength and binding of other metal ions by molecular dynamics (MD) simulations. These studies have allowed questions to be answered, among others, on the function of second shell residues in iron release, the role of synergistic anions in preparing the active site for iron binding, and the differences between the kinetics of the N- and the C-lobe. MD simulations on FbpA have led to the detailed observation of the binding kinetics of phosphate to the apo form, and to the conformational preferences of the holo form under conditions mimicking the environmental niches provided by the periplasmic space. To study the dynamics of these proteins with their receptors, one must resort to coarse-grained methodologies, since these systems are prohibitively large for atomistic simulations. A study of the complex of human transferrin (hTf) with its pathogenic receptor by such methods has revealed a potential mechanistic explanation for the defense mechanism that arises in evolutionary warfare. Meanwhile, the motions in the transferrin receptor bound hTf have been shown to disfavor apo hTf dissociation, explaining why the two proteins remain in complex during the recycling process from the endosome to the cell surface. Open problems and possible technological applications related to metal ion binding-release in iron transport proteins that may be handled by hybrid use of quantum mechanical, MD and coarse-grained approaches are discussed.

Proteins as supramolecular hosts for C60: a true solution of C60 in water

Hybrid systems have great potential for a wide range of applications in chemistry, physics and materials science. Conjugation of a biosystem to a molecular material can tune the properties of the components or give rise to new properties. As a workhorse, here we take a C60@lysozyme hybrid. We show that lysozyme recognizes and disperses fullerene in water. AFM, cryo-TEM and high resolution X-ray powder diffraction show that the C60 dispersion is monomolecular. The adduct is biocompatible, stable in physiological and technologically-relevant environments, and easy to store. Hybridization with lysozyme preserves the electrochemical properties of C60. EPR spin-trapping experiments show that the C60@lysozyme hybrid produces ROS following both type I and type II mechanisms. Due to the shielding effect of proteins, the adduct generates significant amounts of 1O2 also in aqueous solution. In the case of type I mechanism, the protein residues provide electrons and the hybrid does not require addition of external electron donors. The preparation process and the properties of C60@lysozyme are general and can be expected to be similar to other C60@protein systems. It is envisaged that the properties of the C60@protein hybrids will pave the way for a host of applications in nanomedicine, nanotechnology, and photocatalysis.