Interaction of fullerenol with lysozyme investigated by experimental and computational approaches

Conformational Engineering of Flexible Protein Fragments on the Surface of Different Nanoparticles: The Surface-Atom Mobility Rules

As a newly emerging technology, conformational engineering (CE) has been gradually displaying the power of producing protein-like nanoparticles (NPs) by tuning flexible protein fragments into their original native conformation on NPs. But apparently, not all types of NPs can serve as scaffolds for CE. To expedite the CE technology on a broader variety of NPs, the essential characteristic of NPs as scaffolds for CE needs to be identified. Herein, we investigate the potential of two distinct types of NPs as scaffolds for CE: CdSe/ZnS quantum dots (QDs), an ionic compound NP, and palladium NPs (PdNPs), a metal NP. The results demonstrate that while QDs cannot support the restoration of the native conformation and function of the complementary-determining region (CDR) fragments of antibodies, PdNPs can. The notably disparate outcomes unequivocally show that the mobility of the surface atoms/adatoms of the NPs or the mobility of the conjugating bonds to the NPs is essential for CE, which allows the conjugated peptides to undergo a conformational change from their initial random conformation to their most stable native conformation under the constraints mimicking the native long-range interactions in the original proteins. This discovery opens the door for CE on more NPs in the future.

Characterization of the effects of bridging linker on the β-Lactoglobulin binding mechanism on the nanoscale metal-organic frameworks

Revealing the interaction modes between nanoscale metal-organic frameworks (NMOFs) and food matrix is crucial for functional release but it still remains largely unknown to date. This study specifically focused on the milk protein adsorption mechanism of NMOFs using UiO66/UiO66-NH2 and β-lactoglobulin (β-LG) as models. UiO66 and UiO66-NH2 quenched the fluorescence of β-LG via static mechanism. Due to the enhanced electrostatic forces caused by NH2, UiO66-NH2-β-LG (2.83 × 105 mol·L-1) exhibited higher binding constant than UiO66-β-LG (2.61 × 105 mol·L-1), while UiO66 with higher hydrophobicity adsorbed more β-LG. The defects of UiO influenced the binding sites on the β-LG, and the higher the defect degree, the higher the binding energy. For the stability of the system, the H-bonding between UiO66 and SER30/PRO38, and the hydrophobic interaction between UiO66-NH2 and LYS101 played important roles. Furthermore, the secondary structure content of β-LG changed after interacting with both UiO, resulting in reduced density of β-LG.

Versatile applications of fullerenol nanoparticles

Nanomaterials have become increasingly important over time as research technology has enabled the progressively precise study of materials at the nanoscale. Developing an understanding of how nanomaterials are produced and tuned allows scientists to utilise their unique properties for a variety of applications, many of which are already incorporated into commercial products. Fullerenol nanoparticles C60(OH)n, 2 ≤ n ≤ 44 are fullerene derivatives and are produced synthetically. They have good biocompatibility, low toxicity and no immunological reactivity. In addition, their nanometre size, large surface area to volume ratio, ability to penetrate cell membranes, adaptable surface that can be easily modified with different functional groups, drug release, high physical stability in biological media, ability to remove free radicals, magnetic and optical properties make them desirable candidates for various applications. This review comprehensively summarises the various applications of fullerenol nanoparticles in different scientific fields such as nanobiomedicine, including antibacterial and antiviral agents, and provides an overview of their use in agriculture and biosensor technology. Recommendations are also made for future research that would further elucidate the mechanisms of fullerenols actions.

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.

Folding of Flexible Protein Fragments and Design of Nanoparticle-Based Artificial Antibody Targeting Lysozyme

It is generally believed that a protein's sequence solely determines its native structure, but how the long- and short-range interactions jointly determine the native structure/conformation of the protein or every local fragment of the protein is still not fully understood. Since most protein fragments are unstructured on their own, direct observation of the folding of flexible protein fragments is very difficult. Interestingly, we show that it is possible to graft the complementary-determining regions (CDRs) of antibodies onto the surface of a gold nanoparticle (AuNP) to create AuNP-based artificial antibodies (denoted as Goldbodies), such as an antilysozyme Goldbody. Goldbodies can specifically recognize the corresponding antigens like the original natural antibodies do, but direct structural evidence for the refolding or restoration of native conformation of the grafted CDRs on AuNPs is still missing and in high demand. Herein we design a new Goldbody that targets an epitope on the lysozyme different from that of the previous antilysozyme Goldbody, and the one circle of helix in the CDR makes it possible to distinguish the unfolded conformation of the free CDR and its folded conformation on AuNPs by circular dichroism (CD) spectroscopy. The refolding of flexible protein fragments on NPs provides unique evidence and inspiration for understanding the fundamental principles of protein folding.

A potential inhibitor of MDM2 by restoring the native conformation of the p53 α-helical peptide on gold nanoparticles

Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold NPs (AuNPs), and create an AuNP-based anti-MDM2 artificial antibody, denoted as Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism spectra confirm that its α-helical conformation in the original p53 protein is restored on the anti-MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti-MDM2 Goldbody and MDM2, demonstrating the anti-MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen-antibody systems, but can also be applied more widely in other protein-protein interfaces to create more and more artificial proteins for various biomedical applications.

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.

Characterization of the Specific Interactions between Nanoparticles and Proteins at Residue-Resolution by Alanine Scanning Mutagenesis

The interaction between nanoparticles and proteins is a central problem in the nano-bio-fields. However, it is still a great challenge to characterize the specific interaction between nanoparticles and proteins in structural details. Using the Goldbodies, the artificial antibodies created by grafting complementary-determining regions (CDRs) of natural antibodies onto gold nanoparticles, as the models, we manage to identify the key residues of the CDR peptides on gold nanoparticles for the specific interactions by alanine scanning mutagenesis. Each and every residue of the CDR peptides on two Goldbodies (which specifically bind with hen egg white lysozyme and epidermal growth factor receptor, respectively) is mutated to alanine one by one, generating a total of 18 single-mutants of the two Goldbodies. Experimental results reveal that the key residues of the CDR peptides for the specific interactions between the two Goldbodies and the corresponding antigens are exactly the same as those in the natural antibodies, thus proving that the correct conformations of the CDRs of natural antibodies have been successfully reconstructed on AuNPs. This is the first residue-resolution structural illustration for the specific interaction between a designed nanoparticle and a protein.

Influence of Structured Water Layers on Protein Adsorption Process: A Case Study of Cytochrome c and Carbon Nanotube Interactions and Its Implications

Cytochrome c, an essential protein of the electron transport chain, is known to be capable of amplifying the toxicity of carbon nanomaterials via free-radical generation. To understand their interaction, as well as the more general protein-nanoparticle interaction at molecular levels, we investigate the adsorptions between cytochrome c and carbon nanotubes (CNTs) in dynamic and thermodynamic ways using molecular dynamics simulations. The results reveal a well-defined three-phase process separated by two transition points: the diffusion phase where the protein diffuses in the water box, the lockdown phase I where the protein inserts into the surface-bound water layers and rearranges its conformation to fit to the surface of the CNT, and the lockdown phase II where cytochrome c repels the water molecules standing in its way to the surface of CNT and reaches stable adsorption states. The structured water layers affect the movement of atoms by electrostatic forces. In lockdown phase I, the conformation adjustment of the protein dominates the adsorption process. The most thermally favorable adsorption conformation is determined. It shows that except for the deformation of short β sheets and some portions of α helixes, most of the secondary structures of cytochrome c remain unchanged, implying that most of the functions of cytochrome c are preserved. During these processes, the energy contributions of the hydrophilic residues of cytochrome c are much larger than those of hydrophobic residues. Interestingly, the structured water layers at the CNT surface allow more hydrophilic residues such as Lys to get into close contact with the CNT, which plays a significant role during the anchoring process of adsorption. Our results demonstrate that the heme group is in close contact with the CNT in some of the adsorbed states, which hence provides a way for electron transfer from cytochrome c to the CNT surface.

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.

Uptake and Transfer of 13C-Fullerenols from Scenedesmus obliquus to Daphnia magna in an Aquatic Environment

Fullerenol, a water-soluble polyhydroxylated fullerene nanomaterial, enters aquatic organisms and ecosystems through different ingestion exposures and may pose environmental risks. The study of their uptake routes and transfer in aquatic systems is scarce. Herein, we quantitatively investigated the aquatic uptake and transfer of ¹³C-fullerenols from Scenedesmus obliquus to Daphnia magna using ¹³C-skeleton-labeling techniques. The bioaccumulation and depuration of fullerenol in Daphnia magna increased with exposure doses and time, reaching steady state within 16 h in aqueous and feeding-affected aqueous routes. The capacity of Daphnia magna to ingest fullerenol via the aqueous route was much higher than that via the dietary route. From the aqueous to feeding-affected aqueous, the kinetic analysis demonstrated the bioaccumulation factors decreases, which revealed that algae suppressed Daphnia magna uptake of fullerenols. The aqueous route was the primary fullerenols ingestion pathway for Daphnia magna. Kinetic analysis of the accumulation and transfer in Daphnia magna via the dietary route indicated low transfer efficiency of fullerenol along the Scenedesmus obliquus-Daphnia magna food chain. Using stable isotope labeling techniques, these quantitative data revealed that carbon nanomaterials underwent complex aquatic accumulation and transfer from primary producers to secondary consumers and algae inhibited their transfer in food chains.

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.

Exploring the Inhibitory and Antioxidant Effects of Fullerene and Fullerenol on Ribonuclease A

Fullerene-protein interaction studies have been a key topic of investigation in recent times, but the lower water solubility of fullerene somewhat limits its application in the biological system. In this work, we have compared the activities of fullerene and its water-soluble hydrated form, that is fullerenol, on ribonuclease A (RNase A) under physiological conditions (pH 7.4). The interaction studies of fullerene and fullerenol with protein suggest that the binding depends on the hydrophobic interactions between the protein and the ligand. In addition, fullerene and fullerenol slow down the ribonucleolytic activity of RNase A through noncompetitive and mixed types of inhibition, respectively. This precisely gives the idea about the ligand-binding sites in RNase A, which has further been explored using docking studies. Both these nanoparticles show a reduction in dityrosine formation in RNase A caused due to oxidative stress and also prevent RNase A dimer formation to different extents depending on their concentration.

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.

Toxicity of Pristine and Chemically Functionalized Fullerenes to White Rot Fungus Phanerochaete chrysosporium

Fullerenes are widely produced and applied carbon nanomaterials that require a thorough investigation into their environmental hazards and risks. In this study, we compared the toxicity of pristine fullerene (C60) and carboxylated fullerene (C60-COOH) to white rot fungus Phanerochaete chrysosporium. The influence of fullerene on the weight increase, fibrous structure, ultrastructure, enzyme activity, and decomposition capability of P. chrysosporium was investigated to reflect the potential toxicity of fullerene. C60 did not change the fresh and dry weights of P. chrysosporium but C60-COOH inhibited the weight gain at high concentrations. Both C60 and C60-COOH destroyed the fibrous structure of the mycelia. The ultrastructure of P. chrysosporium was changed by C60-COOH. Pristine C60 did not affect the enzyme activity of the P. chrysosporium culture system while C60-COOH completely blocked the enzyme activity. Consequently, in the liquid culture, P. chrysosporium lost the decomposition activity at high C60-COOH concentrations. The decreased capability in degrading wood was observed for P. chrysosporium exposed to C60-COOH. Our results collectively indicate that chemical functionalization enhanced the toxicity of fullerene to white rot fungi and induced the loss of decomposition activity. The environmental risks of fullerene and its disturbance to the carbon cycle are discussed.

In vitro inhibition of pancreatic α-amylase by spherical and polygonal starch nanoparticles

Nanoparticles are novel and fascinating materials for tuning the activities of enzymes.

Fluorescence Behavior of Schiff Base-N, N'-bis(salicylidene) Trans 1, 2-Diaminocyclohexane in Proteinous and Micellar Environments

Fluorescence properties of N, N'-bis(salicylidene) trans 1, 2-diaminocyclohexane (H ₂ L) is used to probe the anionic (SDS), cationic (CTAB) and nonionic (TX-100) micelles as well as in serum albumins (BSA and HSA) and chicken egg white lysozyme (LYZ) by steady state and picosecond time-resolved fluorescence spectroscopy. The fluorescence band intensity was found to increase with concomitant blue-shift with gradual addition of different surfactants. All the experimental results suggest that the probe molecule resides in the micelle-water interface rather than going into the micellar core. However, the penetration is more towards the micellar hydrocarbon core in nonionic surfactant (TX-100) while comparing with ionic surfactants (SDS and CTAB). Several mean microscopic properties such as critical micelle concentration, polarity parameters and binding constant were calculated in presence of different surfactants. The decrease in nonradiative decay rate constants in micellar environments indicates restricted motion of the probe inside the micellar nanocages with increasing fluorescence emission intensity and quantum yields. Further in this work, we also investigated the interaction behavior of the probe with different proteins at low concentrations under physiological conditions (pH = 7.4). Stern-Volmer analysis of the tryptophan (Trp) fluorescence quenching data in presence of probe reveals Stern-Volmer constant (K_sv) as well as bimolecular quenching rate constant (K_q). The binding constant as well as the number of binding sites of the probe with proteins were also monitored and found to be 1:1 stoichiometry ratio.

Characterization of fullerenol-protein interactions and an extended investigation on cytotoxicity

Fullerenols, known as polyhydroxylated derivatives of fullerene, have attracted great attention due to their distinctive material properties and potential applications in biology and medicine. As a step toward the elucidation of basic behavior in biological systems, a variety of spectroscopic measurements as well as isothermal titration calorimetry (ITC) were applied to study the interaction between fullerenol (C₆₀(OH)₄₄) and serum proteins (bovine serum albumin (BSA) and γ-globulins). The results of fluorescence spectra indicated that the intrinsic fluorescence of proteins could be effectively quenched by the dynamic mechanism. The affinity values of both proteins bound to fullerenol were of the same order of magnitude. Meanwhile, ITC results showed that the interaction between fullerenol and BSA was enthalpy favorable, while the interaction with γ-globulins was enthalpy unfavorable. Furthermore, fullerenol had little influence on the secondary structure of both proteins. Additional cytotoxicity tests showed that the presence of proteins attenuated the toxic effect of fullerenol on human normal gastric epithelial cell line (GES-1). Thus, the interaction between fullerenol and proteins is indispensable to evaluate the biosafety of fullerenol, which may in turn promotes the development of its biological applications.

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.

Thermodynamics of hydration of fullerols [C60(OH)n] and hydrogen bond dynamics in their hydration shells

Molecular dynamics simulations of fullerene and fullerols [C₆₀(OH)_n, where n = 2-30] in aqueous solutions have been performed for the purpose of obtaining a detailed understanding of the structural and dynamic properties of these nanoparticles in water. The structures, dynamics and hydration free energies of the solute molecules in water have been analysed. Radial distribution functions, spatial density distribution functions and hydrogen bond analyses are employed to characterize the solvation shells of water around the central solute molecules. We have found that water molecules form two solvation shells around the central solute molecule. Hydrogen bonding in the bulk solvent is unaffected by increasing n. The large decrease in solvation enthalpies of these solute molecules for n > 14 enhances solubilisation. The diffusion constants of solute molecules decrease with increasing n. The solvation free energy of C₆₀ in water is positive (52.8 kJ/mol), whereas its value for C₆₀(OH)₃₀ is highly negative (-427.1 kJ/mol). The effects of surface hydroxylation become more dominant once the fullerols become soluble.

Elucidating the binding efficacy of β-galactosidase on graphene by docking approach and its potential application in galacto-oligosaccharide production

Herein, we propose the synthesis and characterization of graphene for the immobilization of β-galactosidase for improved galacto-oligosaccharide (GOS) production. The size of synthesized graphene was observed to be 25 nm by TEM analysis while interaction of enzyme with the nanosupport was observed by FTIR spectroscopy. Docking was obtained using molecular docking program Dock v.6.5 while the visual analyses and illustration of protein-ligand complex were investigated by utilizing chimera v.1.6.2 and PyMOL v.1.3 softwares. Immobilized β-galactosidase (IβG) showed improved stability against various physical and chemical denaturants. Km of IβG was increased to 6.41 mM as compared to 2.38 mM of soluble enzyme without bringing significant change in Vmax value. Maximum GOS content also registered an increase in lactose conversion. The maximum GOS production was achieved by immobilized enzyme at specific temperature and time. Hence, the developed nanosupport can be further exploited for developing a biosensor involving β-galactosidase or for immobilization of other industrially/therapeutically important enzymes.

Surface modification-mediated biodistribution of ¹³C-fullerene C₆₀ in vivo

BACKGROUND

Functionalization is believed to have a considerable impact on the biodistribution of fullerene in vivo. However, a direct comparison of differently functionalized fullerenes is required to prove the hypothesis. The purpose of this study was to investigate the influences of surface modification on the biodistribution of fullerene following its exposure via several routs of administration.

METHODS

(13)C skeleton-labeled fullerene C60 ((13)C-C60) was functionalized with carboxyl groups ((13)C-C60-COOH) or hydroxyl groups ((13)C-C60-OH). Male ICR mice (~25 g) were exposed to a single dose of 400 μg of (13)C-C60-COOH or (13)C-C60-OH in 200 μL of aqueous 0.9% NaCl solution by three different exposure pathways, including tail vein injection, gavage and intraperitoneal exposure. Tissue samples, including blood, heart, liver, spleen, stomach, kidneys, lungs, brain, large intestine, small intestine, muscle, bone and skin were subsequently collected, dissected, homogenized, lyophilized, and analyzed by isotope ratio mass spectrometry.

RESULTS

The liver, bone, muscle and skin were found to be the major target organs for C60-COOH and C60-OH after their intravenous injection, whereas unmodified C60 was mainly found in the liver, spleen and lung. The total uptakes in liver and spleen followed the order: C60 > > C60-COOH > C60-OH. The distribution rate over 24 h followed the order: C60 > C60-OH > C60-COOH. C60-COOH and C60-OH were both cleared from the body at 7 d post exposure. C60-COOH was absorbed in the gastrointestinal tract following gavage exposure and distributed into the heart, liver, spleen, stomach, lungs, intestine and bone tissues. The translocation of C60-OH was more widespread than that of C60-COOH after intraperitoneal injection.

CONCLUSIONS

The surface modification of fullerene C60 led to a decreased in its accumulation level and distribution rate, as well as altering its target organs. These results therefore demonstrate that the chemical functionalization of fullerene had a significant impact on its translocation and biodistribution properties. Further surface modifications could therefore be used to reduce the toxicity of C60 and improve its biocompatibility, which would be beneficial for biomedical applications.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation - a common strategy for solubilizing and functionalizing fullerene - on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.

Nanoinformatics: emerging databases and available tools

Nanotechnology has arisen as a key player in the field of nanomedicine. Although the use of engineered nanoparticles is rapidly increasing, safety assessment is also important for the beneficial use of new nanomaterials. Considering that the experimental assessment of new nanomaterials is costly and laborious, in silico approaches hold promise. Several major challenges in nanotechnology indicate a need for nanoinformatics. New database initiatives such as ISA-TAB-Nano, caNanoLab, and Nanomaterial Registry will help in data sharing and developing data standards, and, as the amount of nanomaterials data grows, will provide a way to develop methods and tools specific to the nanolevel. In this review, we describe emerging databases and tools that should aid in the progress of nanotechnology research.

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

Integrating carbon nanoparticles (CNPs) with proteins to form hybrid functional assemblies is an innovative research area with great promise for medical, nanotechnology, and materials science. The comprehension of CNP-protein interactions requires the still-missing identification and characterization of the 'binding pocket' for the CNPs. Here, using Lysozyme and C60 as model systems and NMR chemical shift perturbation analysis, a protein-CNP binding pocket is identified unambiguously in solution and the effect of the binding, at the level of the single amino acid, is characterized by a variety of experimental and computational approaches. Lysozyme forms a stoichiometric 1:1 adduct with C60 that is dispersed monomolecularly in water. Lysozyme maintains its tridimensional structure upon interaction with C60 and only a few identified residues are perturbed. The C60 recognition is highly specific and localized in a well-defined pocket.

Self-assembled graphene-dextran nanohybrid for killing drug-resistant cancer cells

A nanohybrid based on nanoscale graphene oxide (NGO) and dextran has been designed and employed for effectively killing drug-resistant MCF-7/ADR cells. This graphene-based nanohybrid was readily prepared through π-π interaction of NGO and hematin-terminated dextran (HDex), being denoted as NGO-HDex. It revealed an improved stability in physiological conditions as compared to native NGO. Besides, NGO-HDex could efficiently load doxorubicin (DOX), an anticancer drug, with drug loading capacity of 3.4 mg/mg NGO and liberate the drug with a pH-dependent profile. Cell viability assay indicated that the NGO-HDex displayed lower cytotoxicity against MCF-7/ADR cells as compared to native NGO. DOX-loaded NGO-HDex, however, revealed more efficient killing effect in the cells than free DOX because the nanohybrid caused a higher amount of DOX accumulated in the cells. The results of this study highlight that the NGO-HDex has high potential for killing drug-resistant cancer cells.

Preparation of graphene adsorbents and their applications in water purification

Graphene has attracted great interest for its unique structure, fantastic properties, and wide applications. Among the various applications, graphene-based materials hold great potential as adsorbents in decontaminating water because of the large surface area, diverse functionalities, ease of preparation, and low cost of treatment. Graphene and its composites have been used in treating heavy metals, dyes, pesticide, antibiotics, oils, and so on. In this paper, we reviewed the preparation methods of graphene adsorbents and their applications in water purification. The adsorption behaviors of contaminates on graphene are summarized. The interactions between graphene and contaminates are discussed, emphasizing the influence of functional groups. We also propose some guidelines in designing high-performance graphene adsorbents from the physicochemical perspective.

Biosafety and bioapplication of nanomaterials by designing protein-nanoparticle interactions

The protein-nanoparticle (NP) interface is a current frontier of multiple disciplines, full of challenges and opportunities. The unique behaviors of nanomaterials (NMs) bring many exciting applications, and also raise safety concerns. Beyond bioapplications, various NMs could also enter human bodies from the environment. When entering human bodies, NPs interact with various biomolecules, especially proteins, forming a protein corona. This protein-NP complex is what the biosystems 'see' and 'respond to'. Therefore, understanding how NPs interact with proteins is crucial for both bioapplications and the biosafety of NMs. In this review, the current understanding of protein-NP interactions is summarized, including the theoretical background, experimental results, and computational progresses. Guidelines for improving bioapplication performance and reducing the potential biosafety hazard of NMs by designing the protein-NP interactions are discussed, along with future directions and challenges in this exciting field.

Advancing risk assessment of engineered nanomaterials: application of computational approaches

Nanotechnology that develops novel materials at size of 100nm or less has become one of the most promising areas of human endeavor. Because of their intrinsic properties, nanoparticles are commonly employed in electronics, photovoltaic, catalysis, environmental and space engineering, cosmetic industry and - finally - in medicine and pharmacy. In that sense, nanotechnology creates great opportunities for the progress of modern medicine. However, recent studies have shown evident toxicity of some nanoparticles to living organisms (toxicity), and their potentially negative impact on environmental ecosystems (ecotoxicity). Lack of available data and low adequacy of experimental protocols prevent comprehensive risk assessment. The purpose of this review is to present the current state of knowledge related to the risks of the engineered nanoparticles and to assess the potential of efficient expansion and development of new approaches, which are offered by application of theoretical and computational methods, applicable for evaluation of nanomaterials.

Binding of single walled carbon nanotube to WT and mutant HIV-1 proteases: analysis of flap dynamics and binding mechanism

Most of the currently treated HIV-1 protease (HIV-PR) inhibitors have been prone to suffer from the mutations associated drug resistance. Therefore, it is necessary to search for potent alternatives against the drug resistance. In the current study we have tested the single-walled carbon nanotube (SWCNT) as an inhibitor in wild type (WT) as well as in three primary mutants (I50V(PR), V82A(PR) and I84V(PR)) of the HIV-1-PR through docking the SWCNT in the active site region, and then performed all-atom MD simulations for the complexes. The conformational dynamics of HIV-PR with a 20 ns trajectory reveals that the SWCNT can effectively bind to the HIV-1-PR active site and regulate the flap dynamics such as maintaining the flap-flap closed. To gain an insight into the binding affinity, we also performed the MM-PBSA based binding free energy calculations for the four HIV-PR/SWCNT complexes. It was observed that, although the binding between the SWCNT and the HIV-PR decreases due to the mutations, the SWCNTs bind to the HIV-PRs 3-5 folds stronger than the most potent HIV-1-PR inhibitor, TMC114. Remarkably, the significant interactions with binding energy higher than 1kcal/mol focus on the flap and active regions, which favors closing flap-flap and deactivating the active residues of the HIV-PR. The flap dynamics and binding strength information for HIV-PR and SWCNTs can help design SWCNT-based HIV-1-PR inhibitors.

Binding of fullerol to human serum albumin: spectroscopic and electrochemical approach

The potential impact of human exposure to carbonaceous nanomaterials in the environment becomes a concerning issue. Here we report on the interaction of fullerol with human serum albumin (HSA) using spectroscopic and electrochemical methods. The water-soluble fullerene derivative (fullerol) was synthesized and characterized by IR, (1)H NMR, TG-DSC, XRD, HR-TEM, etc. The spectroscopic methods show that the fluorescence quenching of HSA by fullerol is the result of the formation of an HSA-fullerol complex. Binding parameters such as ΔG, ΔH and ΔS were calculated, and the quenching constant K(a) at different temperatures was determined using the modified Stern-Volmer equation. The electrochemical experiments further confirmed the conclusions. In addition, the influences of coexisting heavy metal ions have also been studied in the present system. The circular dichroism spectra (CD), 3D fluorescence spectra and FT-IR spectra results suggest that the secondary structure of HSA was changed by fullerol. Based on the site marker competitive experiments, we can predict the possible binding position of fullerol on the HSA was located at the site of sub domain II A. Furthermore, the distance r between donor (HSA) and acceptor (fullerol) was obtained according to the famous fluorescence resonance energy transfer (FRET) mechanism.

Soft interactions at nanoparticles alter protein function and conformation in a size dependent manner

Weak protein-nanoparticle (NP) interactions are studied in a low binding regime as a model for the soft protein corona around nanoparticles in complex biological fluids. Noncovalent, reversible interactions between Subtilisin Carlsberg (SC) and silica NPs shows significant alteration in conformation and enzymatic activity in a NP-size dependent manner. Very weak interactions between SC and silica NPs were revealed by centrifugation-based separations and further supported by small-angle X-ray scattering, while bovine serum albumin was used as a strongly interacting reference. Secondary and tertiary structure changes of SC were studied via circular dichroism and correlated to enzymatic activity where the enzyme kinetics showed a critical role for nanoparticle size.

Fullerene sorting proteins

Proteins bind fullerenes. Hydrophobic pockets can accommodate a carbon cage either in full or in part. However, the identification of proteins able to discriminate between different cages is an open issue. Prediction of candidates able to perform this function is desirable and is achieved with an inverse docking procedure that accurately accounts for (i) van der Waals interactions between the cage and the protein surface, (ii) desolvation free energy, (iii) shape complementarity, and (iv) minimization of the number of steric clashes through conformational variations. A set of more than 1000 protein structures is divided into four categories that either select C(60) or C(70) (p-C(60) or p-C(70)) and either accommodate the cages in the same pocket (homosaccic proteins, from σακκoζ meaning pocket) or in different pockets (heterosaccic proteins). In agreement with the experiments, the KcsA Potassium Channel is predicted to have one of the best performances for both cages. Possible ways to exploit the results and efficiently separate the two cages with proteins are also discussed.