C60@Lysozyme: direct observation by nuclear magnetic resonance of a 1:1 fullerene protein adduct

Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation

Ligand unbinding is mediated by its free energy change, which has intertwined contributions from both energy and entropy. It is important, but not easy, to quantify their individual contributions to the free energy profile. We model hydrophobic ligand unbinding for two systems, a methane particle and a C60 fullerene, both unbinding from hydrophobic pockets in all-atom water. Using a modified deep learning framework, we learn a thermodynamically optimized reaction coordinate to describe the hydrophobic ligand dissociation for both systems. Interpretation of these reaction coordinates reveals the roles of entropic and enthalpic forces as the ligand and pocket sizes change. In both cases, we observe that the free-energy barrier to unbinding is dominated by entropy considerations. Furthermore, the process of methane unbinding is driven by methane solvation, while fullerene unbinding is driven first by pocket wetting and then fullerene wetting. For both solutes, the direct importance of the distance from the binding pocket to the learned reaction coordinate is present, but low. Our framework and subsequent feature important analysis thus give useful thermodynamic insight into hydrophobic ligand dissociation problems that are otherwise difficult to glean.

Interactions between modified fullerenes and proteins in cancer nanotechnology

Fullerenes have numerous properties that fill the gap between small molecules and nanomaterials. Several types of chemical reaction allow their surface to be ornamented with functional groups designed to change them into 'ideal' nanodelivery systems. Improved stability, and bioavailability are important, but chemical modifications can render them practically soluble in water. 'Buckyball' fullerene scaffolds can interact with many biological targets and inhibit several proteins essential for tumorigeneses. Herein, we focus on the inhibitory properties of fullerene nanomaterials against essential proteins in cancer nanotechnology, as well as the use of dedicated proteins to improve the bioavailability of these promising nanomaterials.

Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy

Carboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration.

Identification of Blood Transport Proteins to Carry Temoporfin: A Domino Approach from Virtual Screening to Synthesis and In Vitro PDT Testing

Temoporfin (mTHPC) is one of the most promising photosensitizers used in photodynamic therapy (PDT). Despite its clinical use, the lipophilic character of mTHPC still hampers the full exploitation of its potential. Low solubility in water, high tendency to aggregate, and low biocompatibility are the main limitations because they cause poor stability in physiological environments, dark toxicity, and ultimately reduce the generation of reactive oxygen species (ROS). Applying a reverse docking approach, here, we identified a number of blood transport proteins able to bind and disperse monomolecularly mTHPC, namely apohemoglobin, apomyoglobin, hemopexin, and afamin. We validated the computational results synthesizing the mTHPC-apomyoglobin complex (mTHPC@apoMb) and demonstrated that the protein monodisperses mTHPC in a physiological environment. The mTHPC@apoMb complex preserves the imaging properties of the molecule and improves its ability to produce ROS via both type I and type II mechanisms. The effectiveness of photodynamic treatment using the mTHPC@apoMb complex was then demonstrated in vitro. Blood transport proteins can be used as molecular “Trojan horses” in cancer cells by conferring mTHPC (i) water solubility, (ii) monodispersity, and (iii) biocompatibility, ultimately bypassing the current limitations of mTHPC.

Dissecting the Interactions between Chlorin e6 and Human Serum Albumin

Chlorin e6 (Ce6) is among the most used sensitizers in photodynamic (PDT) and sonodynamic (SDT) therapy; its low solubility in water, however, hampers its clinical exploitation. Ce6 has a strong tendency to aggregate in physiological environments, reducing its performance as a photo/sono-sensitizer, as well as yielding poor pharmacokinetic and pharmacodynamic properties. The interaction of Ce6 with human serum albumin (HSA) (i) governs its biodistribution and (ii) can be used to improve its water solubility by encapsulation. Here, using ensemble docking and microsecond molecular dynamics simulations, we identified the two Ce6 binding pockets in HSA, i.e., the Sudlow I site and the heme binding pocket, providing an atomistic description of the binding. Comparing the photophysical and photosensitizing properties of Ce6@HSA with respect to the same properties regarding the free Ce6, it was observed that (i) a red-shift occurred in both the absorption and emission spectra, (ii) a maintaining of the fluorescence quantum yield and an increase of the excited state lifetime was detected, and (iii) a switch from the type II to the type I mechanism in a reactive oxygen species (ROS) production, upon irradiation, took place.

Quantitative Multistate Binding Model of Silica Nanoparticle-Protein Interactions Obtained from Multinuclear Spin Relaxation

Nanoparticle-assisted NMR spin relaxation (NASR), which makes internal protein dynamics in solution directly observable on nanosecond to microsecond time scales, has been applied to different nuclei and relaxation processes of the same protein system. A model is presented describing the transient interaction between ubiquitin and anionic silica nanoparticles for the unified interpretation of a wealth of experimental data including ²H, ¹³C, and ¹⁵N relaxation of methyl side chain and backbone moieties. The best model, implemented using a stochastic Liouville equation, describes the exchange process via an intermediary encounter state between free and fully nanoparticle-bound protein. The implication of the three-state binding model on the interpretation of NASR data is discussed.

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.

Molecular mechanism of two functional protein structure changes under 2,3-butanedione-induced oxidative stress and apoptosis effects in the hepatocytes

Food security has become closely watched with the occurrence of a series of food safety incidents in recent years. The widespread adoption of 2,3-butanedione (BUT), as a food additive, is an unpreventable significant risk factor to food security. Based on this, mouse hepatocyte AML-12 cells and two functional proteins (bovine serum albumin and lysozyme) were utilized as targeted receptors to study the adverse effects of BUT at the cellular and molecular levels. Results suggested that BUT could disrupt the redox balance of AML-12 cells, reducing glutathione (GSH) activity fell to 87.18 %, which cannot offset the production of reactive oxygen species (ROS). Meanwhile, the increasement of lipid peroxidation and malondialdehyde (MDA) levels were observed. The mitochondrial membrane function was also abnormal due to the excessive accumulation of ROS and eventually leads to cell apoptosis and death. At the molecular level, the exposure of BUT could alter the skeleton and secondary structure of bovine serum albumin (BSA) and lysozyme (LYZ), and it could statically quench the intrinsic fluorescence of proteins. The combined experiments confirmed proved the potentially toxic effects of BUT accumulation on the detoxification organ, providing theoretical support for the liver diseases caused by BUT exposure, and a reference for the risk assessment of occupational exposure of BUT.

Solution NMR methods for structural and thermodynamic investigation of nanoparticle adsorption equilibria

Characterization of dynamic processes occurring at the nanoparticle (NP) surface is crucial for developing new and more efficient NP catalysts and materials. Thus, a vast amount of research has been dedicated to developing techniques to characterize sorption equilibria. Over recent years, solution NMR spectroscopy has emerged as a preferred tool for investigating ligand-NP interactions. Indeed, due to its ability to probe exchange dynamics over a wide range of timescales with atomic resolution, solution NMR can provide structural, kinetic, and thermodynamic information on sorption equilibria involving multiple adsorbed species and intermediate states. In this contribution, we review solution NMR methods for characterizing ligand-NP interactions, and provide examples of practical applications using these methods as standalone techniques. In addition, we illustrate how the integrated analysis of several NMR datasets was employed to elucidate the role played by support-substrate interactions in mediating the phenol hydrogenation reaction catalyzed by ceria-supported Pd nanoparticles.

Fullerenes against COVID-19: Repurposing C60 and C70 to Clog the Active Site of SARS-CoV-2 Protease

The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, Mpro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, Mpro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C70 as an innovative scaffold for the inhibition of SARS-CoV-2 Mpro. At odds with masitinib, both C60 and C70 interact more strongly with SARS-CoV-2 Mpro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to Mpro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding.

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.

Bio-Applications of Multifunctional Melanin Nanoparticles: From Nanomedicine to Nanocosmetics

Bioinspired nanomaterials are ideal components for nanomedicine, by virtue of their expected biocompatibility or even complete lack of toxicity. Natural and artificial melanin-based nanoparticles (MNP), including polydopamine nanoparticles (PDA NP), excel for their extraordinary combination of additional optical, electronic, chemical, photophysical, and photochemical properties. Thanks to these features, melanin plays an important multifunctional role in the design of new platforms for nanomedicine where this material works not only as a mechanical support or scaffold, but as an active component for imaging, even multimodal, and simple or synergistic therapy. The number of examples of bio-applications of MNP increased dramatically in the last decade. Here, we review the most recent ones, focusing on the multiplicity of functions that melanin performs in theranostics platforms with increasing complexity. For the sake of clarity, we start analyzing briefly the main properties of melanin and its derivative as well as main natural sources and synthetic methods, moving to imaging application from mono-modal (fluorescence, photoacoustic, and magnetic resonance) to multi-modal, and then to mono-therapy (drug delivery, anti-oxidant, photothermal, and photodynamic), and finally to theranostics and synergistic therapies, including gene- and immuno- in combination to photothermal and photodynamic. Nanomedicine aims not only at the treatment of diseases, but also to their prevention, and melanin in nature performs a protective action, in the form of nanopigment, against UV-Vis radiations and oxidants. With these functions being at the border between nanomedicine and cosmetics nanotechnology, recently examples of applications of artificial MNP in cosmetics are increasing, paving the road to the birth of the new science of nanocosmetics. In the last part of this review, we summarize and discuss these important recent results that establish evidence of the interconnection between nanomedicine and cosmetics nanotechnology.

Insights into Characterization Methods and Biomedical Applications of Nanoparticle-Protein Corona

Nanoparticles (NPs) exposed to a biological milieu will strongly interact with proteins, forming "coronas" on the surfaces of the NPs. The protein coronas (PCs) affect the properties of the NPs and provide a new biological identity to the particles in the biological environment. The characterization of NP-PC complexes has attracted enormous research attention, owing to the crucial effects of the properties of an NP-PC on its interactions with living systems, as well as the diverse applications of NP-PC complexes. The analysis of NP-PC complexes without a well-considered approach will inevitably lead to misunderstandings and inappropriate applications of NPs. This review introduces methods for the characterization of NP-PC complexes and investigates their recent applications in biomedicine. Furthermore, the review evaluates these characterization methods based on comprehensive critical views and provides future perspectives regarding the applications of NP-PC complexes.

Synthesis and characterization of a reconstituted myoglobin-chlorin e6 adduct for theranostic applications

Chlorin e6 (Ce6) and its derivatives are among the most important photosensitizers in photodynamic therapy. Due to their intense fluorescence, chlorins may also be used for diagnostics. However, low solubility in water and high tendency to aggregation restrict their medical use. Here we demonstrate that apo-myoglobin, by reinserting Ce6 in its heme binding pocket, can be used to monomolecularly disperse it. The reconstructed myoglobin-Ce6 adduct presents noticeable changes in the photophysical properties of the chromophore. A red-shift, in particular in the transparency window, can be observed in the absorption and in the emission spectra of the adduct compared to the spectra of the free chlorin in PBS. The adduct presents a higher quantum yield and an increased excited-state lifetime with respect to the free Ce6. The binding of Ce6 to apo-myoglobin determines a decrease of the 1O2 generation but a three-fold increase of peroxides production, determining globally an increase in the performance of Ce6 as a photosensitizer and imaging agent.

Protein-directed crystalline 2D fullerene assemblies

Water soluble 2D crystalline monolayers of fullerenes grow on planar assemblies of engineered consensus tetratricopeptide repeat proteins. Designed fullerene-coordinating tyrosine clamps on the protein introduce specific fullerene binding sites, which facilitate fullerene nucleation. Through reciprocal interactions between the components, the hybrid material assembles into two-dimensional 2 nm thick structures with crystalline order, that conduct photo-generated charges. Thus, the protein-fullerene hybrid material is a demonstration of the developments toward functional materials with protein-based precision control of functional elements.

Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques

In the last decade, nanoparticles (NPs) have become a key tool in medicine and biotechnology as drug delivery systems, biosensors and diagnostic devices. The composition and surface chemistry of NPs vary based on the materials used: typically organic polymers, inorganic materials, or lipids. Nanoparticle classes can be further divided into sub-categories depending on the surface modification and functionalization. These surface properties matter when NPs are introduced into a physiological environment, as they will influence how nucleic acids, lipids, and proteins will interact with the NP surface. While small-molecule interactions are easily probed using NMR spectroscopy, studying protein-NP interactions using NMR introduces several challenges. For example, globular proteins may have a perturbed conformation when attached to a foreign surface, and the size of NP-protein conjugates can lead to excessive line broadening. Many of these challenges have been addressed, and NMR spectroscopy is becoming a mature technique for in situ analysis of NP binding behavior. It is therefore not surprising that NMR has been applied to NP systems and has been used to study biomolecules on NP surfaces. Important considerations include corona composition, protein behavior, and ligand architecture. These features are difficult to resolve using classical surface and material characterization strategies, and NMR provides a complementary avenue of characterization. In this review, we examine how solution NMR can be combined with other analytical techniques to investigate protein behavior on NP surfaces.

Stable and Biocompatible Monodispersion of C60 in Water by Peptides

The lack of solubility in water and the formation of aggregates hamper many opportunities for technological exploitation of C₆₀. Here, different peptides were designed and synthesized with the aim of monomolecular dispersion of C₆₀ in water. Phenylalanines were used as recognizing moieties, able to interact with C₆₀ through π-π stacking, while a varying number of glycines were used as spacers, to connect the two terminal phenylalanines. The best performance in the dispersion of C₆₀ was obtained with the FGGGF peptidic nanotweezer at a pH of 12. A full characterization of this adduct was carried out. The peptides disperse C₆₀ in water with high efficiency, and the solutions are stable for months both in pure water and in physiological environments. NMR measurements demonstrated the ability of the peptides to interact with C₆₀. AFM measurements showed that C₆₀ is monodispersed. Electrospray ionization mass spectrometry determined a stoichiometry of C₆₀@(FGGGF)₄. Molecular dynamics simulations showed that the peptides assemble around the C₆₀ cage, like a candy in its paper wrapper, creating a supramolecular host able to accept C₆₀ in the cavity. The peptide-wrapped C₆₀ is fully biocompatible and the C₆₀ "dark toxicity" is eliminated. C₆₀@(FGGGF)₄ shows visible light-induced reactive oxygen species (ROS) generation at physiological saline concentrations and reduction of the HeLa cell viability in response to visible light irradiation.

Photodynamic Activity of Fullerene Derivatives Solubilized in Water by Natural-Product-Based Solubilizing Agents

Water-soluble fullerenes prepared by using solubilizing agents based on natural products are promising photosensitizers for photodynamic therapy. Cyclodextrin, β-1,3-glucan, lysozyme, and liposomes can stably solubilize not only C₆₀ and C₇₀ , but also some C₆₀ derivatives in water. To improve the solubilities of fullerenes, specific methods have been developed for each solubilizing agent. Water-soluble C₆₀ and C₇₀ exhibit photoinduced cytotoxicity under near-ultraviolet irradiation, but not at wavelengths over 600 nm, which are the appropriate wavelengths for photodynamic therapy. However, dyad complexes of solubilized C₆₀ derivatives combined with light-harvesting antenna molecules improve the photoinduced cytotoxicities at wavelengths over 600 nm. Furthermore, controlling the fullerene and antenna molecule positions within the solubilizing agents affects the performance of the photosensitizer.

Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C60-Lysozyme Model

Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.

Monitoring characteristics and genotoxic effects of engineered nanoparticle-protein corona

Engineered nanoparticles (ENPs) possess different physical and chemical properties compared to their bulk counterparts. These unique properties have found application in various products in the area of therapeutics, consumer goods, environmental remediation, optical and electronic fields. This has also increased the likelihood of their release into the environment thereby affecting human health and ecosystem. ENPs, when in contact with the biological system have various physical and chemical interactions with cellular macromolecules including proteins. These interactions lead to the formation of protein corona around the ENPs. Consequently, living systems interact with the protein-coated ENP rather than with a bare ENP. This ENP-protein interaction influences uptake, accumulation, distribution and clearance and thereby affecting the cytotoxic and genotoxic responses. Although there are few studies which discussed the fate of ENPs, there is a need for extensive research in the field of ENPs, to understand the interaction of ENPs with biological systems for their safe and productive application.

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.

C60 Bioconjugation with Proteins: Towards a Palette of Carriers for All pH Ranges

The high hydrophobicity of fullerenes and the resulting formation of aggregates in aqueous solutions hamper the possibility of their exploitation in many technological applications. Noncovalent bioconjugation of fullerenes with proteins is an emerging approach for their dispersion in aqueous media. Contrary to covalent functionalization, bioconjugation preserves the physicochemical properties of the carbon nanostructure. The unique photophysical and photochemical properties of fullerenes are then fully accessible for applications in nanomedicine, sensoristic, biocatalysis and materials science fields. However, proteins are not universal carriers. Their stability depends on the biological conditions for which they have evolved. Here we present two model systems based on pepsin and trypsin. These proteins have opposite net charge at physiological pH. They recognize and disperse C60 in water. UV-Vis spectroscopy, zeta-potential and atomic force microscopy analysis demonstrates that the hybrids are well dispersed and stable in a wide range of pH’s and ionic strengths. A previously validated modelling approach identifies the protein-binding pocket involved in the interaction with C60. Computational predictions, combined with experimental investigations, provide powerful tools to design tailor-made C60@proteins bioconjugates for specific applications.

Specific Interaction Sites Determine Differential Adsorption of Protein Structural Isomers on Nanoparticle Surfaces

In biological systems, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric ubiquitin (Ub) dimers by NPs was investigated by solution NMR spectroscopy. Lys63- and Lys48-linked Ub₂ were adsorbed by large anionic NPs with different affinities, whereas the binding strength was similar in the cases of smaller particles. After the incorporation of paramagnetic tags into NPs, the observed site-resolved paramagnetic footprints provided a high-resolution map of the different protein surfaces binding to NPs. The approach described could be extended to further protein isoforms and more specialized NP systems to allow better control of the interactions between NPs and protein targets.

Fullerene derivatives act as inhibitors of leukocyte common antigen based on molecular dynamics simulations

Fullerene-based molecules are being studied as potential inhibitors of protein tyrosine phosphatases due to their unique properties and low toxicity. However, the underlying molecular mechanism remains elusive. In this study, molecular dynamics (MD) simulations in conjunction with molecular docking calculations were utilized to investigate the binding effects of C₆₀, C₆₀(NH₂)₃₀, and C₆₀(OH)₃₀ on the enzymatic activity of CD45 (a receptor-like protein tyrosine phosphatase). Our results show that all the investigated molecules can be docked into the region between D1 and D2 domains of CD45, and stabilize the protein structure. The average number of residues that directly interact with the C₆₀(NH₂)₃₀ is two more than that of C₆₀(OH)₃₀, F819 and F820 (located in the loop connects α3 and β12), resulting in different effects of C₆₀(NH₂)₃₀ and C₆₀(OH)₃₀ on protein activity. Detailed MD simulation analyses show that transformation of the interaction network caused by C₆₀(NH₂)₃₀ is completely different from that of the control simulation due to the misfolding of α3. Furthermore, the movement of D1 active pocket and KNRY motif are most severely impaired by docking with C₆₀(NH₂)₃₀. Our simulation results illustrate that fullerene derivatives modified with amino groups exhibit conspicuous tumor inhibition to protein tyrosine phosphatases, and can act as effective inhibitors. Our results give insight into the inhibitory effects of fullerene-based molecules on protein tyrosine phosphatases and providing a theoretical basis for the design of effective inhibitors.

Fullerene-based molecules are being studied as potential inhibitors of protein tyrosine phosphatases due to their unique properties and low toxicity.

Modified denatured lysozyme effectively solubilizes fullerene c60 nanoparticles in water

Fullerenes, allotropic forms of carbon, have very interesting pharmacological effects and engineering applications. However, a very low solubility both in organic solvents and water hinders their use. Fullerene C60, the most studied among fullerenes, can be dissolved in water only in the form of nanoparticles of variable dimensions and limited stability. Here the effect on the production of C60 nanoparticles by a native and denatured hen egg white lysozyme, a highly basic protein, has been systematically studied. In order to obtain a denatured, yet soluble, lysozyme derivative, the four disulfides of the native protein were reduced and exposed cysteines were alkylated by 3-bromopropylamine, thus introducing eight additional positive charges. The C60 solubilizing properties of the modified denatured lysozyme proved to be superior to those of the native protein, allowing the preparation of biocompatible highly homogeneous and stable C60 nanoparticles using lower amounts of protein, as demonstrated by dynamic light scattering, transmission electron microscopy and atomic force microscopy studies. This lysozyme derivative could represent an effective tool for the solubilization of other carbon allotropes.

Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose

Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. Here we explore their characteristics that could make them prospective leads for known disease-related proteins. High-throughput virtual screening supported by comprehensive multi-software protein-ligand docking simulation and cheminformatics approaches has been applied in investigation of interactions of 1117 proteins with a 169 fullerene nanoparticles decorated with different small molecules. Moreover, obtained docking results were confirmed by the series of unrestricted all-atom molecular dynamics (MD) simulations. Hydrophobicity of fullerene core along with hydrophilic interaction of side chains plays a key role in binding with the studied proteins. We identified a series of nanoparticles that can lead to development of robust drugs for target proteins and another series that can behave as a highly toxic agent. The structure-activity relationship analysis revealed two significant molecular properties responsible for the binding score values. The application of carefully selected computational techniques and described outcome of the study facilitate development of functional fullerene nanoparticles for drug-like and drug delivery applications.

Competitive Inhibition Mechanism of Acetylcholinesterase without Catalytic Active Site Interaction: Study on Functionalized C60 Nanoparticles via in Vitro and in Silico Assays

Acetylcholinesterase (AChE) activity regulation by chemical agents or, potentially, nanomaterials is important for both toxicology and pharmacology. Competitive inhibition via direct catalytic active sites (CAS) binding or noncompetitive inhibition through interference with substrate and product entering and exiting has been recognized previously as an AChE-inhibition mechanism for bespoke nanomaterials. The competitive inhibition by peripheral anionic site (PAS) interaction without CAS binding remains unexplored. Here, we proposed and verified the occurrence of a presumed competitive inhibition of AChE without CAS binding for hydrophobically functionalized C₆₀ nanoparticles (NPs) by employing both experimental and computational methods. The kinetic inhibition analysis distinguished six competitive inhibitors, probably targeting the PAS, from the pristine and hydrophilically modified C₆₀ NPs. A simple quantitative nanostructure-activity relationship (QNAR) model relating the pocket accessible length of substituent to inhibition capacity was then established to reveal how the geometry of the surface group decides the NP difference in AChE inhibition. Molecular docking identified the PAS as the potential binding site interacting with the NPs via a T-shaped plug-in mode. Specifically, the fullerene core covered the enzyme gorge as a lid through π-π stacking with Tyr72 and Trp286 in the PAS, while the hydrophobic ligands on the fullerene surface inserted into the AChE active site to provide further stability for the complexes. The modeling predicted that inhibition would be severely compromised by Tyr72 and Trp286 deletions, and the subsequent site-directed mutagenesis experiments proved this prediction. Our results demonstrate AChE competitive inhibition of NPs without CAS participation to gain further understanding of both the neurotoxicity and the curative effect of NPs.

Influence of graphene oxide and reduced graphene oxide on the activity and conformation of lysozyme

The dramatically different bio-effects of graphene and graphene oxide (GO) have been widely observed in diverse biological systems, which determine the applications and toxicity of graphene materials. To elucidate the mechanism at molecular level, it is urgent to investigate the enzyme-graphene interaction and its consequences. In this study, we comparatively studied the influence of GO and reduced GO (RGO) on the activity and conformation of lysozyme to provide better understandings of their different bio-effects. Both GO and RGO adsorbed large quantities of lysozyme after incubation. GO inhibited lysozyme activity seriously, while RGO nearly had no influence on the enzyme activity. The different inhibitions of enzyme activity could be explained by the lysozyme conformational changes, where GO induced more changes to the protein conformation according to UV-vis absorbance, far-UV circular dichroism spectra, intrinsic fluorescence quenching, and infrared spectra. Based on the spectroscopic changes of lysozyme, GO induced the loss of secondary structure and exposed the active site of lysozyme more to the aqueous environment. In addition, neither GO nor RGO induced the fibrillation of lysozyme after 12d incubation. The results collectively indicated that the oxidation degree significantly impacted the enzyme-graphene interaction. The implications to the designs of enzyme-graphene system for bio-related applications and the toxicological effects of graphene materials are discussed.

C60@lysozyme: a new photosensitizing agent for photodynamic therapy

C₆₀@lysozyme showed significant visible light-induced singlet oxygen generation in a physiological environment, indicating the potential of this hybrid as an agent for photodynamic therapy.

Residue-Specific Interactions of an Intrinsically Disordered Protein with Silica Nanoparticles and their Quantitative Prediction

Elucidation of the driving forces that govern interactions between nanoparticles and intrinsically disordered proteins (IDP) is important for the understanding of the effect of nanoparticles in living systems and for the design of new nanoparticle-based assays to monitor health and combat disease. The quantitative interaction profile of the intrinsically disordered transactivation domain of p53 and its mutants with anionic silica nanoparticles is reported at atomic resolution using nuclear magnetic spin relaxation experiments. These profiles are analyzed with a novel interaction model that is based on a quantitative nanoparticle affinity scale separately derived for the 20 natural amino acids. The results demonstrate how the interplay of attractive and repulsive Coulomb interactions with hydrophobic effects is responsible for the sequence-dependent binding of a disordered protein to nanoparticles.

Aqueous solubilization of C60 fullerene by natural protein surfactants, latherin and ranaspumin-2

C60 fullerene is not soluble in water and dispersion usually requires organic solvents, sonication or vigorous mechanical mixing. However, we show here that mixing of pristine C60 in water with natural surfactant proteins latherin and ranaspumin-2 (Rsn-2) at low concentrations yields stable aqueous dispersions with spectroscopic properties similar to those previously obtained by more vigorous methods. Particle sizes are significantly smaller than those achieved by mechanical dispersion alone, and concentrations are compatible with clusters approximating 1:1 protein:C60 stoichiometry. These proteins can also be adsorbed onto more intractable carbon nanotubes. This promises to be a convenient way to interface a range of hydrophobic nanoparticles and related materials with biological macromolecules, with potential to exploit the versatility of recombinant protein engineering in the development of nano-bio interface devices. It also has potential consequences for toxicological aspects of these and similar nanoparticles.

Mechanochemical Encapsulation of Fullerenes in Peptidic Containers Prepared by Dynamic Chiral Self-Sorting and Self-Assembly

Molecular capsules composed of amino acid or peptide derivatives connected to resorcin[4]arene scaffolds through acylhydrazone linkers have been synthesized using dynamic covalent chemistry (DCC) and hydrogen-bond-based self-assembly. The dynamic character of the linkers and the preference of the peptides towards self-assembly into β-barrel-type motifs lead to the spontaneous amplification of formation of homochiral capsules from mixtures of different substrates. The capsules have cavities of around 800 Å(3) and exhibit good kinetic stability. Although they retain their dynamic character, which allows processes such as chiral self-sorting and chiral self-assembly to operate with high fidelity, guest complexation is hindered in solution. However, the quantitative complexation of even very large guests, such as fullerene C60 or C70 , is possible through the utilization of reversible covalent bonds or the application of mechanochemical methods. The NMR spectra show the influence of the chiral environment on the symmetry of the fullerene molecules, which results in the differentiation of diastereotopic carbon atoms for C70 , and the X-ray structures provide unique information on the modes of peptide-fullerene interactions.

Blocking the passage: C60 geometrically clogs K(+) channels

Classical molecular dynamics (MD) simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and molecular mechanic/Poisson-Boltzmann surface area (MM-PBSA) energy calculations reveal that C60 may block K(+) channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ∼21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in solvent accessible surface area upon C60 binding shows that binding at this site is governed purely by shape complementarity, and that the molecular determinants of binding are conserved in the entire family of K(+) channels. The presence of this high-affinity binding site conserved among different K(+) channels may have serious implications for the toxicity of carbon nanomaterials.

The study of transient protein-nanoparticle interactions by solution NMR spectroscopy

The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nanobio interfaces. Nanoparticles exhibit unique structures and properties, often different from the corresponding bulk materials, and the nature of their interactions with biological systems remains poorly characterized. Solution NMR spectroscopy is a mature technique for the investigation of biomolecular structure, dynamics, and intermolecular associations, however its use in protein-nanoparticle interaction studies remains scarce and highly challenging, particularly due to unfavorable hydrodynamic properties of most nanoscale assemblies. Nonetheless, recent efforts demonstrated that a number of NMR observables, such as chemical shifts, signal intensities, amide exchange rates and relaxation parameters, together with newly designed saturation transfer experiments, could be successfully employed to characterize the orientation, structure and dynamics of proteins adsorbed onto nanoparticle surfaces. This review provides the first survey and critical assessment of the contributions from solution NMR spectroscopy to the study of transient interactions between proteins and both inorganic (gold, silver, and silica) and organic (polymer, carbon and lipid based) nanoparticles. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin

The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with (15)N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.

Buckybomb: Reactive Molecular Dynamics Simulation

Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material.

Graphene can wreak havoc with cell membranes

Molecular dynamics--coarse grained to the level of hydrophobic and hydrophilic interactions--shows that small hydrophobic graphene sheets pierce through the phospholipid membrane and navigate the double layer, intermediate size sheets pierce the membrane only if a suitable geometric orientation is met, and larger sheets lie mainly flat on the top of the bilayer where they wreak havoc with the membrane and create a patch of upturned phospholipids. The effect arises in order to maximize the interaction between hydrophobic moieties and is quantitatively explained in terms of flip-flops by the analysis of the simulations. Possible severe biological consequences are discussed.

Potential toxicity of graphene to cell functions via disrupting protein-protein interactions

While carbon-based nanomaterials such as graphene and carbon nanotubes (CNTs) have become popular in state-of-the-art nanotechnology, their biological safety and underlying molecular mechanism is still largely unknown. Experimental studies have been focused at the cellular level and revealed good correlations between cell's death and the application of CNTs or graphene. Using large-scale all-atom molecular dynamics simulations, we theoretically investigate the potential toxicity of graphene to a biological cell at molecular level. Simulation results show that the hydrophobic protein-protein interaction (or recognition) that is essential to biological functions can be interrupted by a graphene nanosheet. Due to the hydrophobic nature of graphene, it is energetically favorable for a graphene nanosheet to enter the hydrophobic interface of two contacting proteins, such as a dimer. The forced separation of two functional proteins can disrupt the cell's metabolism and even lead to the cell's mortality.

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

Thiscritical reviewpresents a detailed overview of the chemico-physical principles ruling the non-covalent association between proteins and fullerene, carbon nanotubes and graphene towards the creation of fascinating and innovative hybrid materials for biotechnological applications.

Structural study of a small molecule receptor bound to dimethyllysine in lysozyme

Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx₄) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH₃⁺ to Lys-NH(Me₂)⁺. Of the six possible dimethyllysine sites, sclx₄ selected Lys116-Me₂ and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me₂ residues to form cation-π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me₂ in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.