High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study

The antifouling performance of polymer brushes usually improves with increasing hydrophilicity of the grafted polymer. However, in some cases, less hydrophilic polymers show comparable or better antifouling performance than do more hydrophilic polymers. We investigate the mechanism of this anomalous behavior using molecular dynamics (MD) simulations of coarse-grained (CG) models of weakly and strongly hydrophilic polymers. The antifouling performance is evaluated from the potential of mean force of a model protein. The strongly hydrophilic polymer exhibits a better antifouling performance than the weakly hydrophilic polymer when the substrate of the polymer brush is repulsive. However, when the substrate is sufficiently attractive, the weakly hydrophilic polymer brush becomes more effective than the strongly hydrophilic brush in a certain range of grafting density. This is because the weakly hydrophilic polymer chains form a tightly packed layer that prevents the adsorbate molecule from contacting the substrate. We also perform all-atom (AA) MD simulations for several standard polymers to examine the correspondence with the CG polymer models. The weakly hydrophilic CG polymer is found to be similar to poly[N-(2-hydroxypropyl)methacrylamide] and poly(2-hydroxyethyl methacrylate), both of which have a hydroxyl group in a monomer unit. The strongly hydrophilic CG polymer resembles zwitterionic poly(carboxybetaine methacrylate). A discussion referring to the adsorption free energies of proteins on surfaces calculated in previous AA MD studies suggests that the higher antifouling performance of less hydrophilic polymer brushes can be realized for various combinations of protein and surface.

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Theoretical study of protein adsorption on graphene/h-BN heterostructures

The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.

The Hybrid Nano-Biointerface between Proteins/Peptides and Two-Dimensional Nanomaterials

In typical protein-nanoparticle surface interactions, the biomolecule surface binding and consequent conformational changes are intermingled with each other and are pivotal to the multiple functional properties of the resulting hybrid bioengineered nanomaterial. In this review, we focus on the peculiar properties of the layer formed when biomolecules, especially proteins and peptides, face two-dimensional (2D) nanomaterials, to provide an overview of the state-of-the-art knowledge and the current challenges concerning the biomolecule coronas and, in general, the 2D nano-biointerface established when peptides and proteins interact with the nanosheet surface. Specifically, this review includes both experimental and simulation studies, including some recent machine learning results of a wide range of nanomaterial and peptide/protein systems.

Nanobio Interface Between Proteins and 2D Nanomaterials

Two-dimensional (2D) nanomaterials have significantly contributed to recent advances in material sciences and nanotechnology, owing to their layered structure. Despite their potential as multifunctional theranostic agents, the biomedical translation of these materials is limited due to a lack of knowledge and control over their interaction with complex biological systems. In a biological microenvironment, the high surface energy of nanomaterials leads to diverse interactions with biological moieties such as proteins, which play a crucial role in unique physiological processes. These interactions can alter the size, surface charge, shape, and interfacial composition of the nanomaterial, ultimately affecting its biological activity and identity. This review critically discusses the possible interactions between proteins and 2D nanomaterials, along with a wide spectrum of analytical techniques that can be used to study and characterize such interplay. A better understanding of these interactions would help circumvent potential risks and provide guidance toward the safer design of 2D nanomaterials as a platform technology for various biomedical applications.

Dynamic photoelectrical regulation of ECM protein and cellular behaviors

Dynamic regulation of cell-extracellular matrix (ECM)-material interactions is crucial for various biomedical applications. In this study, a light-activated molecular switch for the modulation of cell attachment/detachment behaviors was established on monolayer graphene (Gr)/n-type Silicon substrates (Gr/Si). Initiated by light illumination at the Gr/Si interface, pre-adsorbed proteins (bovine serum albumin, ECM proteins collagen-1, and fibronectin) underwent protonation to achieve negative charge transfer to Gr films (n-doping) through π-π interactions. This n-doping process stimulated the conformational switches of ECM proteins. The structural alterations in these ECM interactors significantly reduced the specificity of the cell surface receptor-ligand interaction (e.g., integrin recognition), leading to dynamic regulation of cell adhesion and eventual cell detachment. RNA-sequencing results revealed that the detached bone marrow mesenchymal stromal cell sheets from the Gr/Si system manifested regulated immunoregulatory properties and enhanced osteogenic differentiation, implying their potential application in bone tissue regeneration. This work not only provides a fast and feasible method for controllable cells/cell sheets harvesting but also gives new insights into the understanding of cell-ECM-material communications.

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A light-activated molecular switch for regulation of cell attachment/detachment behaviors was established on (Gr/Si) substrates.

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Light-induced charge transfer from ECM protein to Gr/Si through π-π interactions, resulting in the conformational alteration of ECM proteins.

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Structural changes in ECM weakened the binding between RGD and integrin, inducing cell detachment.

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This work provides a feasible method for cell harvesting and improves the understanding of cell-ECM-material communications.

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Effect of Secondary Structures on the Adsorption of Peptides onto Hydrophobic Solid Surfaces Revealed by SALDI-TOF and MD Simulations

The adsorption of peptides and proteins on hydrophobic solid surfaces has received considerable research attention owing to their wide applications to biocompatible nanomaterials and nanodevices, such as biosensors and cell adhesion materials with reduced nanomaterial toxicity. However, fundamental understandings about physicochemical hydrophobic interactions between peptides and hydrophobic solid surfaces are still unknown. In this study, we investigate the effect of secondary structures on adsorption energies between peptides and hydrophobic solid surfaces via experimental and theoretical analyses using surface-assisted laser desorption/ionization-time-of-flight (SALDI-TOF) and molecular dynamics (MD) simulations. The hydrophobic interactions between peptides and hydrophobic solid surfaces measured via SALDI-TOF and MD simulations indicate that the hydrophobic interaction of peptides with random coil structures increased more than that of peptides with an α-helix structure when polar amino acids are replaced with hydrophobic amino acids. Additionally, our study sheds new light on the fundamental understanding of the hydrophobic interaction between hydrophobic solid surfaces and peptides that have diverse secondary structures.

Adsorption of Peptides onto Carbon Nanotubes Grafted with Poly(ethylene Oxide) Chains: A Molecular Dynamics Simulation Study

Carbon nanotubes (CNTs) display exceptional properties that predispose them to wide use in technological or biomedical applications. To remove the toxicity of CNTs and to protect them against undesired protein adsorption, coverage of the CNT sidewall with poly(ethylene oxide) (PEO) is often considered. However, controversial results on the antifouling effectiveness of PEO layers have been reported so far. In this work, the interactions of pristine CNT and CNT covered with the PEO chains at different grafting densities with polyglycine, polyserine, and polyvaline are studied using molecular dynamics simulations in vacuum, water, and saline environments. The peptides are adsorbed on CNT in all investigated systems; however, the adsorption strength is reduced in aqueous environments. Save for one case, addition of NaCl at a physiological concentration to water does not appreciably influence the adsorption and structure of the peptides or the grafted PEO layer. It turns out that the flexibility of the peptide backbone allows the peptide to adopt more asymmetric conformations which may be inserted deeper into the grafted PEO layer. Water molecules disrupt the internal hydrogen bonds in the peptides, as well as the hydrogen bonds formed between the peptides and the PEO chains.

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

Organic contaminants and atmospheric nitrogen at the graphene-water interface: a simulation study

Ordered nanoscale patterns have been observed by atomic force microscopy at graphene-water and graphite-water interfaces. The two dominant explanations for these patterns are that (i) they consist of self-assembled organic contaminants or (ii) they are dense layers formed from atmospheric gases (especially nitrogen). Here we apply molecular dynamics simulations to study the behavior of dinitrogen and possible organic contaminants at the graphene-water interface. Despite the high concentration of N₂ in ambient air, we find that its expected occupancy at the graphene-water interface is quite low. Although dense (disordered) aggregates of dinitrogen have been observed in previous simulations, our results suggest that they are stable only in the presence of supersaturated aqueous N₂ solutions and dissipate rapidly when they coexist with nitrogen gas near atmospheric pressure. On the other hand, although heavy alkanes are present at only trace concentrations (micrograms per cubic meter) in typical indoor air, we predict that such concentrations can be sufficient to form ordered monolayers that cover the graphene-water interface. For octadecane, grand canonical Monte Carlo suggests nucleation and growth of monolayers above an ambient concentration near 6 μg m^-3, which is less than some literature values for indoor air. The thermodynamics of the formation of these alkane monolayers includes contributions from the hydration free-energy (unfavorable), the free-energy of adsorption to the graphene-water interface (highly favorable), and integration into the alkane monolayer phase (highly favorable). Furthermore, the peak-to-peak distances in AFM force profiles perpendicular to the interface (0.43-0.53 nm), agree with the distances calculated in simulations for overlayers of alkane-like molecules, but not for molecules such as N₂, water, or aromatics. Taken together, these results suggest that ordered domains observed on graphene, graphite, and other hydrophobic materials in water are consistent with alkane-like molecules occupying the interface.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.

Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response

The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.

Surface Functionalization of Graphene-Based Materials: Biological Behavior, Toxicology, and Safe-By-Design Aspects

The increasing exploitation of graphene-based materials (GBMs) is driven by their unique properties and structures, which ignite the imagination of scientists and engineers. At the same time, the very properties that make them so useful for applications lead to growing concerns regarding their potential impacts on human health and the environment. Since GBMs are inert to reaction, various attempts of surface functionalization are made to make them reactive. Herein, surface functionalization of GBMs, including those intentionally designed for specific applications, as well as those unintentionally acquired (e.g., protein corona formation) from the environment and biota, are reviewed through the lenses of nanotoxicity and design of safe materials (safe-by-design). Uptake and toxicity of functionalized GBMs and the underlying mechanisms are discussed and linked with the surface functionalization. Computational tools that can predict the interaction of GBMs behavior with their toxicity are discussed. A concise framing of current knowledge and key features of GBMs to be controlled for safe and sustainable applications are provided for the community.

Development of an open-source thermally stabilized quartz crystal microbalance instrument for biomolecule-substrate binding assays on gold and graphene

The interaction of biomolecules, such as proteins, with biomaterial surfaces is key to disease diagnostic and therapeutic development applications. There is a significant need for rapid, low-cost, field-serviceable instruments to monitor such interactions, where open-source tools can help to improve the accessibility to disease screening instruments especially in low- and middle-income countries. We have developed and evaluated a low-cost integrated quartz crystal microbalance (QCM) instrument for biomolecular analysis based on an open-source QCM device. The custom QCM instrument was equipped with a custom-made electronically controlled isothermal chamber with a closed-loop control routine. A thermal coefficient of 5.6 ppm/°C was obtained from a series of evaluations of the implemented control. Additionally, a custom-designed data acquisition system and a mathematical processing and analysis tool is implemented. The quartz crystal detection chips used here incorporate gold and reduced graphene oxide (rGO) coated surfaces. We demonstrate the system capability to monitor and record the biomolecular interaction between a typical protein bovine serum albumin (BSA) and these two substrates. This instrument was compared to a commercial QCM, demonstrating good correspondence between the computed mass adsorption density responses using the Sauerbrey model. For both Au and rGO surfaces, the custom QCM significantly outperforms the commercial system in limit of detection, sensitivity and linear range. The instrument presented here has the potential to serve as a ubiquitous bioelectronic tool for point-of-care disease screening and rapid therapeutics development.

Restricted binding of a model protein on C3N4 nanosheets suggests an adequate biocompatibility of the nanomaterial

The fixed binding pattern of protein adsorption to C₃N₄ plays a major role in the nanomaterial biocompatibility, which results from the inherent porous surface structure.

Bioadhesion in the oral cavity and approaches for biofilm management by surface modifications

BACKGROUND

All soft and solid surface structures in the oral cavity are covered by the acquired pellicle followed by bacterial colonization. This applies for natural structures as well as for restorative or prosthetic materials; the adherent bacterial biofilm is associated among others with the development of caries, periodontal diseases, peri-implantitis, or denture-associated stomatitis. Accordingly, there is a considerable demand for novel materials and coatings that limit and modulate bacterial attachment and/or propagation of microorganisms.

OBJECTIVES AND FINDINGS

The present paper depicts the current knowledge on the impact of different physicochemical surface characteristics on bioadsorption in the oral cavity. Furthermore, it was carved out which strategies were developed in dental research and general surface science to inhibit bacterial colonization and to delay biofilm formation by low-fouling or "easy-to-clean" surfaces. These include the modulation of physicochemical properties such as periodic topographies, roughness, surface free energy, or hardness. In recent years, a large emphasis was laid on micro- and nanostructured surfaces and on liquid repellent superhydrophic as well as superhydrophilic interfaces. Materials incorporating mobile or bound nanoparticles promoting bacteriostatic or bacteriotoxic properties were also used. Recently, chemically textured interfaces gained increasing interest and could represent promising solutions for innovative antibioadhesion interfaces. Due to the unique conditions in the oral cavity, mainly in vivo or in situ studies were considered in the review.

CONCLUSION

Despite many promising approaches for modulation of biofilm formation in the oral cavity, the ubiquitous phenomenon of bioadsorption and adhesion pellicle formation in the challenging oral milieu masks surface properties and therewith hampers low-fouling strategies.

CLINICAL RELEVANCE

Improved dental materials and surface coatings with easy-to-clean properties have the potential to improve oral health, but extensive and systematic research is required in this field to develop biocompatible and effective substances.

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface

Phosphorene, a monolayer of black phosphorus, has emerged as one of the most promising two-dimensional (2D) nanomaterials for various applications in the post-graphene-discovery period due to its highly anisotropic structure and novel properties. In order to apply phosphorene in biomedical fields, it is crucial to understand how it interacts with biomolecules. Herein, we use both molecular dynamics (MD) simulations and experimental techniques to investigate the interactions of phosphorene with a dsDNA segment. Our results reveal that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations. Moreover, the binding strength of dsDNA with phosphorene is found to be mild and does not cause significant distortion in the internal structure of dsDNA. This phenomenon is attributed to the weaker dispersion interaction between dsDNA and phosphorene. Further analysis of the free energy profile calculated by the umbrella sampling technique suggests that the puckered surface morphology significantly reduces the adsorption free energy of DNA bases to phosphorene. Compared to graphene, phosphorene is found to show a milder attraction to DNA, which is confirmed by our electrophoresis experiments. We believe that these findings provide valuable insight into the molecular interactions between phosphorene and dsDNA which may prompt further investigation of phosphorene for future biomedical applications.

Electrospun poly(vinyl alcohol)/reduced graphene oxide nanofibrous scaffolds for skin tissue engineering

Graphene is composed of a two-dimensional (2D) layer of carbon atoms arranged in a honeycomb lattice configuration. In this paper, we adopted a green synthetic method of producing reduced graphene oxide using glucose as a reducing and stabilizing agent. We also investigated the fabrication of electrospun nanofibers of glucose-reduced graphene oxide (GRGO) (0-1.0 wt%) reinforced with polyvinyl alcohol (PVA) as (PG) scaffolds, and chemically crosslinked with acidic glutaraldehyde (GA) in acetone medium to mimic the extracellular matrix (ECM) for skin tissue engineering applications. These PG scaffolds were evaluated for morphology, mechanical strength, surface wettability, thermal properties, hemocompatibility, and biocompatibility. Field emission-scanning electron microscopy (FE-SEM) revealed an increase in the thickness of nanofibers in PG scaffolds with an increase in the concentration of GRGO. X-ray diffraction and attenuated total reflectance-infrared and Raman spectra showed the GRGO was incorporated in the PVA nanofibrous matrix. As the concentration of GRGO was increased in PG scaffolds, tensile strengths and elongations at break decreased, whereas thermal properties increased. The biological activities of PG scaffolds were evaluated using in vitro hemolysis, using CCD-986Sk (a human skin fibroblast cell line) viability and proliferation assays, and by live/dead cell imaging. Results showed GRGO inclusion in PVA nanofibers caused a slight hydrophilic to hydrophobic shift. PG scaffolds did not cause hemolysis of red blood cells even at a GRGO loading of 1.0 wt%, and PG-1.0 scaffold (with a GRGO loading of 1.0 wt%) exhibited excellent compatibility with fibroblasts and significantly increased metabolic activity after culture for 21 days as compared with PG-0 controls. DAPI staining and live/dead imaging assays showed that all PG scaffolds increased fibroblast proliferation and viability, indicating the potential for skin tissue engineering applications.

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.

Nanomaterial Effects on Viral Infection

The potential for environmental and occupational exposures of populations to nanomaterials (NMs) has fostered concerns of associated adverse health effects, with a particular emphasis on pulmonary injury and disease. Many studies have revealed that several types of NMs can evoke a variety of biological responses, such as pulmonary inflammation and oxidative stress, which contribute to allergy, fibrosis, and granuloma formation. Less attention has been paid to health effects that may result from exposure to NMs and additional stressors such as pathogens, with a particular focus on susceptibility to viral infection. This chapter will summarize the current body of literature related to NMs and viral exposures with a primary focus on immune modulation. A summary of the studies performed and major findings to date will be discussed, highlighting proposed molecular mechanisms behind NM-driven host susceptibility, challenges, limitations, and future research needs. Specific mechanisms discussed include direct interaction between NMs and biological molecules, activation of pattern recognition receptors (PRRs) and related signaling pathways, production of oxidative stress and mitochondrial dysfunction, inflammasome activation, and modulation of lipid signaling networks.

Chaperone Like Attributes of Biogenic Fluorescent Gold Nanoparticles: Potential to Alleviate Toxicity Induced by Intermediate State Fibrils Against Neuroblastoma Cells

In general, neurodegenerative disorders have a great deal of correlation with the misfolded as well as aggregated forms of protein-based macromolecules. Among various species formed during the aggregation process, protein oligomers have been classified as most toxic entities against several types of living cells. A series of chemicals have been developed to inhibit protein aggregation as a measure to regulate neurodegenerative diseases. Recently, various classes of nanoparticles have also been reported to inhibit protein aggregation. In the present study, we synthesized fluorescent gold nanoparticles (B-AuNPs) employing Olax scandens leaf extract. Next, an in vitro study was performed to assess the effect of as-synthesized B-AuNPs on the aggregation behavior of the ovalbumin (OVA) and other related model proteins. We performed an extensive study to elucidate anti-amyloidogenic properties of nano-sized entities and established that small-sized B-AuNPs manifest chaperone potential against protein aggregation. Further, we exploited as-synthesized B-AuNPs as a mean to prevent protein aggregation mediated toxicity in neuroblastoma cells.

Adsorption of amino acids on graphene: assessment of current force fields

We compare the free energies of adsorption (ΔAads) and the structural preferences of amino acids on graphene obtained using the non-polarizable force fields-Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid-graphene interactions are favorable irrespective of the force field. While the magnitudes of ΔAads differ between the force fields, the relative free energy of adsorption across amino acids is similar for the studied force fields. ΔAads positively correlates with amino acid-graphene and negatively correlates with graphene-water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that the force fields studied will give qualitatively consistent relative strength of adsorption across proteins but different structural preferences in the graphene adsorbed state.

An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study

Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.

Protein G selects two binding sites for carbon nanotube with dissimilar behavior; a molecular dynamics study

BACKGROUND

Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure.

METHODS

Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized.

RESULTS

Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the first (PGB-CNT1) and the aromatic residues in the second (PGB-CNT2) surface patch. Displacement of amino acids in the PGB-CNT2 complex occurred during the simulation and it caused an increase in its stability at the end of simulation. The amino acids' displacements diminished the PGB α-helix structure by breakage of hydrogen bonds and generated more transient structures. Principal component analysis determined that the interaction of the CNT with the second surface patch of the PGB raised the extent and modes of the PGB motions. In contrast, insignificant structural changes induced in the PGB while the CNT bonded through the first surface patch.

CONCLUSION

Even though neither of the PGB-CNT complexes could prevent structural changes in the PGB, development of the PGB-CNT1 complex induce slight structural changes in its fragment of crystallizable receptor (FCR). Dissimilar structural changes induced in the PGB-CNT complexes are possibly related to various characteristics of the PGB binding sites.

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.

Nature-Inspired Construction of Two-Dimensionally Self-Assembled Peptide on Pristine Graphene

Peptide assemblies have received significant attention because of their important role in biology and applications in bionanotechnology. Despite recent efforts to elucidate the principles of peptide self-assembly for developing novel functional devices, peptide self-assembly on two-dimensional nanomaterials has remained challenging. Here, we report nature-inspired two-dimensional peptide self-assembly on pristine graphene via optimization of peptide-peptide and peptide-graphene interactions. Two-dimensional peptide self-assembly was designed based on statistical analyses of >10⁴ protein structures existing in nature and atomistic simulation-based structure predictions. We characterized the structures and surface properties of the self-assembled peptide formed on pristine graphene. Our study provides insights into the formation of peptide assemblies coupled with two-dimensional nanomaterials for further development of nanobiocomposite devices.

Insight into the Electrical Double Layer of an Ionic Liquid on Graphene

Graphene is a promising next-generation conducting material with the potential to replace traditional electrode materials in supercapacitors. Since energy storage in supercapacitors relies on the electrolyte-electrode interface, here we elucidate the interfacial subnanometer structure of a single component liquid composed solely of cations and anions – an ionic liquid- on electrified graphene. We study the effect of applied potential on the interaction between graphene and a silicon tip in an ionic liquid and describe it within the framework of the Derjaguin-Landau-Verwey-Overbeck (DLVO) theory. The energy is stored in an electrical double layer composed of an extended Stern layer, which consists of multiple ion layers over ~2 nanometers, beyond which a diffuse layer forms to compensate the applied potential on graphene. The electrical double layer significantly responds to the applied potential, and it shows the transition from overscreening to crowding of counterions at the interface at the highest applied potentials. It is proposed that surface charging occurs through the adsorption of the imidazolium cation to unbiased graphene (likely due to π-π interactions) and that the surface potential is better compensated when counterion crowding happens. This study scrutinizes the electrified graphene-ionic liquid interface, with implications not only in the field of energy storage, but also in lubrication.

Single-probe multistate detection of DNA via aggregation-induced emission on a graphene oxide platform

Graphene and graphene oxides (GO), or their reduced forms, have been introduced in a variety of biosensing platforms and have exhibited enhanced performance levels in these forms. We herein report a DNA sensing platform consisting of aggregation-induced emission (AIE) molecules and complementary DNA (comDNA) adsorbed on GO. We experimentally turned the AIE molecule on and off by adjusting its distance, which correlates with DNA structures as shown in our computational results, from the GO sheet, which quenches depending on its distance from the graphene plane. The changes in florescence are reproducible, which demonstrates the probe's ability to identify the binding state of the DNA. Our molecular dynamics simulation results reveal strong π-π interactions between single-strand DNA (ssDNA) and GO, which enable the ssDNA molecule to move closer to the graphene oxide. This reduces the center of mass and binding free energies in the simulation. When hybridized with comDNA, the increased distance, evidenced by the reduced interaction, eliminates the quenching effect and turns on the AIE molecule. Our protocol use of the AIE molecule as a probe thus avoids the complicated steps involved in covalent functionalization and allows the rapid and label-free detection of DNA molecules.

STATEMENT OF SIGNIFICANCE

A simple, rapid method of fluorescent measurement of DNA hybridization in the presence of graphene (oxide) is presented. Conventional fluorescent dyes offer high performance in biosensors. However, labeling procedures are synthetically demanding in time and resources making it less cost-effective. Molecules with aggregation-induced-emission (AIE) property have advantages over traditional fluorescent molecules because of their intrinsic preference for detection as a turn-on probe and their single-molecule detection ability. Previous work has shown AIE dyes act as excellent "label-free" bioprobes with high sensitivity but with limited selectivity. Graphene oxide (GO) with its unique optical properties and affinity to different kinds of biomolecules can be used as an auxiliary to enhance selectivity of AIE dyes. In this work, we report a label-free strategy to detect DNA of particular sequence by water-soluble AIE probes with the aid of GO, supported by the computational explanations for this phenomenon.

Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.

Modeling and simulation of protein-surface interactions: achievements and challenges

Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

Graphene/graphene oxide and their derivatives in the separation/isolation and preconcentration of protein species: A review

The distinctive/unique electrical, chemical and optical properties make graphene/graphene oxide-based materials popular in the field of analytical chemistry. Its large surface offers excellent capacity to anchor target analyte, making it an powerful sorbent in the adsorption and preconcentration of trace level analyte of interest in the field of sample preparation. The large delocalized π-electron system of graphene framework provides strong affinity to species containing aromatic rings, such as proteins, and the abundant active sites on its surface offers the chance to modulate adsorption tendency towards specific protein via functional modification/decoration. This review provides an overview of the current research on graphene/graphene oxide-based materials as attractive and powerful adsorption media in the separation/isolation and preconcentration of protein species from biological sample matrixes. These practices are aiming at providing protein sample of high purity for further investigations and applications, or to achieve certain extent of enrichment prior to quantitative assay. In addition, the challenges and future perspectives in the related research fields have been discussed.

Prediction and clarification of structures of (bio)molecules on surfaces

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.

Hemoglobin-carbon nanotube derived noble-metal-free Fe5C2-based catalyst for highly efficient oxygen reduction reaction

High performance non-precious cathodic catalysts for oxygen reduction reaction (ORR) are vital for the development of energy materials and devices. Here, we report an noble metal free, Fe₅C₂ nanoparticles-studded sp² carbon supported mesoporous material (CNTHb-700) as cathodic catalyst for ORR, which was prepared by pyrolizing the hybrid adduct of single walled carbon nanotubes (CNT) and lyophilized hemoglobin (Hb) at 700 °C. The catalyst shows onset potentials of 0.92 V in 0.1 M HClO₄ and in 0.1 M KOH which are as good as commercial Pt/C catalyst, giving very high current density of 6.34 and 6.69 mA cm⁻² at 0.55 V vs. reversible hydrogen electrode (RHE), respectively. This catalyst has been confirmed to follow 4-electron mechanism for ORR and shows high electrochemical stability in both acidic and basic media. Catalyst CNTHb-700 possesses much higher tolerance towards methanol than the commercial Pt/C catalyst. Highly efficient catalytic properties of CNTHb-700 could lead to fundamental understanding of utilization of biomolecules in ORR and materialization of proton exchange membrane fuel cells for clean energy production.

Antibody-based affinity cryo-EM grid

The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states.

Novel insights into l-cysteine adsorption on transition metal doped graphene: influences of the dopant and the vacancy

Unprotonated l-cysteine is docked on single-vacancy and double-vacancy graphenes doped with transition metals from Sc to Zn. The adsystems exhibit interesting adsorption stability and magnetism.

Multifunctional cell-culture platform for aligned cell sheet monitoring, transfer printing, and therapy

While several functional platforms for cell culturing have been proposed for cell sheet engineering, a soft integrated system enabling in vitro physiological monitoring of aligned cells prior to their in vivo applications in tissue regeneration has not been reported. Here, we present a multifunctional, soft cell-culture platform equipped with ultrathin stretchable nanomembrane sensors and graphene-nanoribbon cell aligners, whose system modulus is matched with target tissues. This multifunctional platform is capable of aligning plated cells and in situ monitoring of cellular physiological characteristics during proliferation and differentiation. In addition, it is successfully applied as an in vitro muscle-on-a-chip testing platform. Finally, a simple but high-yield transfer printing mechanism is proposed to deliver cell sheets for scaffold-free, localized cell therapy in vivo. The muscle-mimicking stiffness of the platform allows the high-yield transfer printing of multiple cell sheets and results in successful therapies in diseased animal models. Expansion of current results to stem cells will provide unique opportunities for emerging classes of tissue engineering and cell therapy technologies.

Interlayer water regulates the bio-nano interface of a β-sheet protein stacking on graphene

Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a β-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by water molecules. The interlayer water filled within interstices of the bio-nano interface could suppress the molecular vibration of surface groups on protein, and could impair the CH···π interaction driving the attraction of the protein and graphene. The intermolecular coupling of interlayer water would be relaxed by the relative motion of protein upon graphene due to the interaction between water and protein surface. This effect reduced the hindrance of the interlayer water against the assembly of protein on graphene, resulting an appropriate adsorption status of protein on graphene with a deep free energy trap. Thereby, the confinement and the relative sliding between protein and graphene, the coupling of protein and water, and the interaction between graphene and water all have involved in the modulation of behaviors of water molecules within the bio-nano interface, governing the hindrance of interlayer water against the protein assembly on hydrophobic graphene. These results provide a deep insight into the fundamental mechanism of protein adsorption onto graphene surface in water.

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.